Ok, so you're saying you are rotating the compressor cover down so it will align with the stock location intercooler right? Meaning the compressor covers discharge would be pointing straight ahead? I have seen where some have had to cut the water pump discharge tube for the S hose down slightly in order to get the compressor cover to rotate down. I actually did this on my old grey car running a PT74 GTQ with a stock water pump, I had to rotate my compressor cover past straight ahead to meet up with the pipe I was running that did not have the 90* bend in it. I just stuffed a rag into the hole and carefully trimmed the water pump nipple shorter using a dremel tool and a shop vac to keep the shavings from flying around. Reinstall the S hose and clamp it down, The comp cover would barely touch the hose, but I was able to rotate it down further to meet up to the IC pipe. You might have to do this also, especially if your turbo has the newer style cover that has the Precision logo casted into the discharge of the compressor cover. The newer style comp cover is slightly larger than the older style H cover. They came out with the new logo style H cover at the end of 2005. Also, you might have to get a new wastegate actuator that has the correct bracket welded to it, if you are running an internal style downpipe. If not and you're running an external wastegate style setup, then you should be ok.
HTH
Patrick