Things to watch out for

Down Pipe:
It is easiest to find a TQC downpipe and use that since it bolts up to the stock exhaust location at the catalytic converter and clears all the undercarriage.  The actual downpipe ends two inches further to the rear of the car, but the catalitic converter is 2" shorter, so the exhausts line up perfectly.  If this is not available, a 5kt downpipe can be used, but the passenger-side floor pan will have to be bent in for the 5kt down pipe to fit properly.  Some people have reported that the 5kt downpipe does in fact fit, but with a very tight clearance, so hammering in part of the floor pan is still a good idea.  Others have reported clearance problems between the 5kt downpipe and the 4kq subframe requiring a little custom bending of the down pipe.  This may be due to the differences in the automatic and manual transmision parts.  The one from the auto. trans. goes further out to the rear of the engine bay before making the downward bend, while the downpipe from a manual trans. car goes down sooner providing more clearance.  It must be noted, however, that the 5kt downpipe will not bolt up to the exhaust in the stock location, so a custom welding job may be needed to join it and the rest of the exhaust.

Intake Manifold:
The 5000 turbo intake manifold that most closely matches the TQC intake manifold is that of a 1984 or 1985 5kt.  These have the forward facing oval throttle body just like the TQC and should be used in conjunction with the TQC intercooler.   They are reported as been nearly identical, with the socket for the intake air temperature sensor built in.  Later 5kt's have a different intake manifold with a round oppening with a small triangular corner and are missing the socket for the intake temperature sensor as it was mounted on the intercooler outlet on these cars - it should be used in conjunction with the 5kt intercooler mounted up front. Very early 5kt's have the throttle body facing the rear of the engine and should be avoided.  Basicly, if you are using a TQC intercooler, use the TQC or '84-'85 intake manifold.  If you have an intercooler mounted in front, use a '86-'88 intake manifold.

Intake air temperature sensor:
Both the TQC and the 5000 turbo computers need an input from an intake air temperature sensor.  On the TQC and the '84-'85 5kt, this sensor is mounted directly in the intake manifold.  On the later (>'86) 5000 turbo cars, this sensor was moved to the intercooler.  If you are using a TQC or '84-'85 5kt intake manifold, you don't have to worry a whole lot about this, but if you are using a later 5kt manifold, you will either have to fabricate a socket for the temp. sensor on the manifold, or find a place to put it between the intercooler outlet and the throttle (if you put it at the inlet, the computer would receive an erroneous signal since the intake air is colder after it goes thru the intercooler).  Of course, if you are using the 5kt intercooler, you can simply put the sensor in its place.

Flywheel/clutch:
Any 5kt or 200 flywheel/clutch will bolt up to the 4kq tranny, so this is not a big issue.  Although the standard 4kq clutch is a heavy duty unit, it is not necessarily up to the task of handling forced-induction duties.  Best to use a 5ktq clutch and flywheel.  One caveat:  the TQC and the 5000t/200 flywheels have the reference pins for the computer RPM and reference signals at different locations, so only a TQC flywheel will work with a TQC computer and a 5000t flywheel will have to be used with a 5000t computer.  They are not interchangeable.  The TDC reference pin is one tooth more advanced on the TQC flywheel, so if you use a 5kt flywheel with the TQC computer, the timing wilt be retarded about 2-3 degs. and if you use a TQC flywheel with a 5kt computer, the timing will be advanced 2-3 degs.  The two magnetic senders on the clutch side of the flywheel are not used for anything except testing at the factory.  Also, the TQC flyweel is VERY heavy (>30 lbs).  In comparison, the 4kq flywheel weighs 22 lbs. The lightest will be that off a 200, weighing in at 14-15 lbs.

How much does the 5kt flywheel weighs?

Airbox:
The easiest thing to do here is (again) to find a TQC top for the airbox (part #035-133-845) and turn the 5kt metering unit around, using the TQC fuel meter-to-turbo-inlet hose.  This part is reportedly available from the dealer.  In this case, the stock 4kq lower half of the airbox can be kept in place, with a little modifications to remove the thremostatic flap that receives hot air from the exhaust manifold.  Some people have reported using the 5kt fuel metering unit/distributor on the 4kq airbox, but requiring cutting of some portions of the right fender.  In this case, the 5kt bellow that goes over the flap and the pipe that goes to the turbo intake should be used. Whatever you do, make sure that the airbox has a cool air supply and is not sucking hot air from around the turbo.  The exhaust manifold glows cherry red after a good run and is in close proximity to the airbox.  Some heat shielding in this area is a great idea.

TQC airbox top half:  part #035-133-845)
TQC aluminum spout (over the meter flap): part #035-133-837AB
Complete TQC airbox: part #035-133-357

Radiators and hoses:
Some people are running their stock radiators, some suggest upgrading to the dual radiator set-up of the 80/90 5-cyl. cars. Reportedly, the late '87 Coupe GT with the electronic dash had the same auxiliary radiator as used in the TQC.  If you do decide to put the intercooler in front, then you would be giving up the space for the auxiliary radiator.  In any case you want to make sure that it is clean in the inside for good heat transfer.  If you plan on keeping the air conditioner, some air conditioner compressor are bigger than others.  Make sure it fits witout moving the radiator, or be prepared to move it back a little.  A helper pusher fan in front of the condenser/radiator is not a bad idea either.  The coolant jackets on the side of the head, where the upper radiator hose attaches, are the same for both the 4kq, TQC, and 5kt's, so there shouldn't be any problems here.

If you are using a water-cooled turbo with after-run pump (highly recomended), you will have to make provisions for the coolant line going to/from this pump.  I heard that there was a Volvo kit used to retrofit a water cooled turbo into an older car wich previously had an air/oil cooled turbo.  Perhaps it can be usefull here as well.  Another option is to use the 5kt upper radiator hose that has the tee built in for the turbo coolant recirculation pump.  A small peice of pipe will be needed to join this to the half of a std. hose since the tee hose isn't long enough to reach the head.

Heater:
Reportedly, the heater pipes are located in the same spot accross these engines, so there shouldn't be any problems geting the heater to work.  In any case, the heater pipe from the old engine can be reused with the 5kt engine.  The heater valve does not interfere with anything, but should be situated carefully to avoid it been too close to the wastegate.

Air Conditioning:
Using the stock 4kq alternator location, air conditioning will be lost to make space for the turbo and plumbing.  To some people in the upper latitudes this is of little importance.  However, for those of us that have to endure 110 degree summers, air conditioning is extremely important.  The work around is to obtain a donor engine with the alternator and compressor still attached and use them.  On the 5kt and the TQC, the alternator is on the right side of the engine and the compressor is on the radiator side. New hoses may need to be fabricated, but any competent A/C service shop should be able to do this.  If this is the case, the alternator wiring will have to be modified accordingly to reach the new location.  Remember to change the dryer and consider possibly upgrading to an R-12 replacement while you're at it.

Alternator:
The old alternator can be reused and kept on the stock location if A/C is not important.  If you want air conditioner in the car, the alternator will have to be moved to the right side like the 5kt cars (might as well keep the 5kt alternator and brackets) and the wiring will have to be modified accordingly (see: air conditioning)

Are the alternator plugs the same - ie, will 5kt alternator accept the 4kq wiring,
or wil the 5kt alternator wiring have to be spliced in as well?

Intercooler:
Either get a TQC intercooler or do some custom job with whatever you can find.  Some people have used a 5kt intercooler and hoses, others have used one from a Porsche 944t.  Be prepared to do some cutting and welding on the way.  This can be a potential show stopper for the not so mechanically gifted. 5kt intercoolers incorporate a socket for installing the intake air temp. sensor on the outlet.  If you are using a TQC or '84-'85 5kt intake manifold, you can move this sensor over there and plug the hole.  If you are using a later 5000t intake manifold, you will have to put the sensor in this location and make sure it doesn't interfere with anything.  Whatever you do, remember that this sensor has to be on the outlet side of the intercooler (see:  intake air temperature sensor, intake manifold).   Some people have gone as far as installing the intercooler in front of the radiator/condenser trying to avoid cutting too much metal off the frond end.

Oil Cooler:
An oil cooler will have to be mounted in a custom location.  It is very important to keep the oil cooler since the turbo engine needs all the cooling it can get and the turbo really gets the oil really hot.  The Audi turbo engines have the thermostatic flage to insure that the oil gets up to operating temperature regardless of outside temperature and has a chance to burn any water or contaminants that may have dissolved into the oil. The 5kt cooler has some very long lines: it could be used, but may be easier to do a custom job

Oil Pan:
The stock 4kq oil pan can be swapped into the new engine.  If you can get your hands on an Audi 200 oil pan, it has improved baffling and reportedly clears the radiator.  The regular 5kt oil pan will interfere with the radiator.

200 20v oil pan: part #034-103-599B   $260 from Linda @ Carlsen
200 10v oil pan: part #054-103-601A   $82     "       "               "

Can anyone confirm whether or not the 5kt oil pan does in fact fit?

Engine Mounts/Brackets:
The engine mounting brackets in a 5kt engine will have to be swapped for the old 4kq ones. At the same time, put the 5kt motor mounts with the heat shields.  Some have said that S4 mounts are better, but is is unclear why.

Battery:
The battery will have to be relocated to the right well in the trunk (unless you want to be creative and stuff it under the seat in a custom welded battery box) to make room for the wastegate.  A BIG wire will have to be routed from the trunk trhough under the carpet on the right, to the engine bay by means of the A/C openings.  Make sure the wire insulation does not rub against any metal part, or you could have a monster short!  For this reason, it would be prudent to put a fusible link right at the + battery connection.  The battery tray will have to be removed or at least partially cut to make space for the wastegate.  It may be usefull to but a jumper block like the 5kt cars in the engine bay as well.  Another alternative is to run the battery cable under the car together with the fuel lines.  You won't have to worry about routing it under the carpet and may be quicker, but it is more exposed. to the elements.

Ignition Coil:

Might as well use the ignition coil of the donor engine as well.

Tie rods:
The right tie rod will have to be substituted for a TQC unit in order to clear the turbo/wastegate plumbing.  The ends are not replaceable and are too big (won't fit the 4kq struts), so something will have to be done so that the TQC tie rod can accept the 4kq tie rod ends (weld the end of a 4k tie rod to the TQC part).  Some people report bending the stock 4kq tie rod to clear the wastegate.

What is the part no. of the TQC tie right tie rod?

Throttle cable:
You may need a longer 5kt throttle cable, as the 4kq cable may be too short.  Beware, however, that the end of the cables are not identical meaning that some work will be needed to attach the 5kt cable to the gass pedal.

Any other comments?

Brakes/hydraulic system:
There are a couple of options here.  One is to simply retain the stock 4kq power steering pump and the vacuum assisted brakes and rely on the off-throttle vacuum for assist.  A vacuum reservoir can be added to help with left foot braking. Something else that can be done is to take the 4kq cylinder head (that has the vacuum pump that runs off the camshaft) and replace the exhaust valves with 5kt sodium-filled exhaust valves, although some people have cautioned that the combustion chambers are not identical.  The other option is to have a machine shop work on the 5kt head to make it accept the vacuum pump.  Finally (not recommended) you can swap all the hydraulic system off a TQC (including pump, steering rack, brake master cylinder, reservoir) into the 4kq.  A new brake fluid reservoir will need to be placed somewhere for the clutch.  The power steering lines shouldn't interfere with anything.
 
Are the combustion chambers the same on the 4kq and the 5kt heads (are the any problems here)?
Are the exhaust manifold studs the same, or are the turbo head studs larger?

Wiring Harness:
If you use an old 5kt engine, it is really simple; only a couple of wires need to be added into the wiring harness.  On the other hand, if you use an MC engine, a lot of wires will need to be integrated into this wiring harness.  This can be a really time consuming task and you will need wiring schematics for both the 5kt and the 4kq.  The dashboard may need to be removed to do all this.  Best to take your time and solder every connection and splice.  Don't even think about using those cheap quick connectors.  It may be easier to get a 5kt ECU wiring harness (right wiring harness) and completely replace the old CIS-E wiring harness.