CIS-E can run boost, you will need to retard your base timing for ignition or get an MSD timing retard system. You would want to get a pressure switch to hook up to the intake manifold and wire it into the WOT switch wiring. You'll need to add extra fuel as well, you'll want to adjust the bas pressure for the DPR. There is instructions on doing it here.\\
http://forums.vwvortex.com/showthread.php?3070507
"Take the DPR from the car and place it in the palm of your hand in a folded-over shop rag. The rag is there to protect your skin in the event of flathead screwdriver slippage. Unscrew the brass flathead screw from the back of the DPR. The threads on this screw are amazingly fine. It is a marvel to me that such a screw could even be made. Remove the screw and KEEP TRACK OF THE COPPER WASHER. If you lose this washer, you will be looking for another DPR.
Behind this screw is a small allen head (VERY rarely this screw is actually a very small flathead) setscrew. This screw is what you adjust to power tune CIS-E. Just as with the idle mixture screw, small adjustments are significant, and just as with the idle screw, CW enriches. A good initial adjustment is 1/4 turn CW. Turn the screw, then re-tighten the flathead screw and reassemble the DPR to the metering head and reconnect the DPR along with the test harness. Don't go nuts tightening the screws that hold the DPR onto the metering head. They don't require that much torque and they may well be coming right back off after a brief test drive.
Fire up the engine. The idle mixture that you just set a few minutes ago will now be way rich. As always, wait for the O2 sensor to heat up before making any adjustments. Once the O2 sensor is warmed up, the idle current will drop substantially, possibly to zero. Make small CCW tweaks on the idle mixture screw until current is back to spec. Continue running engine until cooling fan has cycled once. Once engine is fully warm and idle mixture is set, take the car for a test drive with the test harness connected and routed into the car for a passenger to read while under low-load cruising and acceleration conditions.
On the test drive, you are looking for a nice rich 12:1 if possible AFR under WOT/boost and a middle of the road amperage to the DPR under light cruising throttle. When the system is near the end of its range of adjustment, cruising amperage to the DPR will become very low. At the point that the cruising amperage touches zero, the ECU will no longer be able to make lean-out adjustments to correct light-load mixtures. Adjusting the system beyond this will cause poor economy with negligible (if any) power increases.
Repeat the above DPR adjustment procedure as necessary with this caveat: DPR adjustments from this point can be VERY touchy, so no more than a 1/8 turn increment per adjustment is advisable. Each time you adjust the DPR, you re-start the engine, warm it up and set idle mixture again as described above before driving.
So far, I have found that 1/4 turn is all a stock engine needs to reach its full potential on CIS-E with a WOT switch. A 2L/big valve head/mild cam/good exhaust setup usually can take about 1/2 turn. A SUPER wild NA engine or turbo engine can use all the fuel it can get before the system can no longer adjust light load mixture--usually 3/4 turn. Beyond this, the system can usually no longer maintain a good stoich-ish mixture under light load."
more details in the thread obviously. The DPR is the part on the fuel distributor with the 2 wire connector, the 2 wire one is a potentiometer for the metering head position.
You can also turn it up some to make more power on the stock motor.
Before you mess with it though, make sure to find and fix all of the vacuum leaks, do a tune up, using ngk v power plugs. This includes all of the adjustments in the bentley for ignition timing, idle speed, co mixture etc. If you want a pdf copy of a bentley, i have one for a scirocco, it's the same engine so those things will be the same, although you have a ce2 wiring system so the wiring isnt the same going into the car's body harness.