Without any circuit diagrams etc here at home I will be of limited assistance but I'll give you some basics. I'm assuming that you have a complete Gen VII kit with harness and software V 4.0.0. In your application you do not need the factory ECM. The Gen VII's red fuel pump wire comes from its own relay meaning that it goes to +12V when active and can go directly to a fuel pump. Find your cars FP relay and cut wire to fuel pump, solder this wire to wire that runs to FP. The Gen VII's fan wire is not relayed and goes to 0V when active, like your car's original fan signal. Just find the fan relay and substitute this wire instead of your orig PCM's fan signal wire. Can't remember, but if your car has two fans, the Gen VII can control them idividually. At WOT the Gen VII turns your fan(s) off.
There are companies who sell adaptors for Gen VIIs that eliminate their harness and allow direct plug in to the car's harness, much easier. I've hard-wired several Gen VIIs into factory harnesses, much harder but neat installation. Where's your EMIC (Accel/DFI Engine Management Installation Center) that sold you your system, I'm doing their job.