OK. Answer this... when you get the truck to crank but not start is the "security" light (not your aftermarket LED in the dash bezel) flash? You stated you swapped out the ignition switch right? Well, if you did swap that out and the PK2 light is flashing then you have to relearn the PK2 code. You have to crank it over but leave the ignition on for 11 minutes then do it again. If it doesn't start, do it once more. It may take over 30 minutes but you have to crank it over, not just leave it on.
You should take ALL the aftermarket stuff out especially since you have no fobs to even use it. Just trace the wires. Take the shroud off of the column. You should be able to trace those bypass wires to the PK2 system. The PK2 wires should be tiny 22 gauge wires that are yellow, orange/black, and white with the white one not tapped into.