The cylinder heads do play a part in compression, as their combustion chamber volume is part of the calculation. You can find good calculators online to help you make your decision.
I'd need someone to verify, but I seem to recall that the 2003 GT motors come with a 18cc dish piston and come in at around 9 and half compression. If you can swap to a deeper dish (like 23 or 24), your compression should drop to around 8 and a half, but that's assuming stock heads. I think the stock PI heads have a combustion chamber volume of 42cc, so if your new heads have more, your compression will drop a bit just from that.
96 GT - Triple Black, Lowered - Full PI Swap, P&P Heads, Off-Road H-Pipe, Flowmasters
Current Project: 86 GT Hatch