The FSwerks instructions are good, but not great. The ones i have are for a stage 1 install, so they dot address an intercooler.....but they also do not include instructions for the diverter valve/diverter vacuum or the water lines.
The water lines.....you need to cut your upper heater hose. It runs from your passenger firewall to the top of the engine where the trans bolts up. Cut it in half and plumb one waterline into one end and the other into the other end. Dont the instructions say "DO NOT START YOUR CAR UNTIL YOU HAVE A TUNE IN?"