I had this problem and spent about 2 weeks going over the wires, looking up the diagrams, and testing stuff in my car. Everything tested good but it just didn't work. I disconnected my battery for a couple days while doing something else to my car and to my surprise the next time I drove my car it was working again. I don't know what caused it but if everything checks out then try disconnecting the battery for a couple days.
Old setup: D1SC @ 11psi, FMIC, TR 224/227 .560/.560 114 lsa cam, Ported TB, Hooker LT's/ORY, Corsa Cat Back , 275/60/15 MT Drag Radials on Prostars, various supporting mods... didn't last long on the stock shortblock
New setup: F1A @ 14-16psi, TSP 402, AFR 225's, 232/240 .595/.608 115 lsa cam, AIS Meth system, Nasty Stage 3 Fuel System, Spec stage 5 clutch, PST Drive shaft, Moser 9", BMR suspension... numbers comming soon.