That's really vague and hard to even start on, especially since it's a swap job and not in the original truck... What year/options is the donor truck? How about the recipient vehicle? Were both vehicles originally a manual (did the trans come from the donor also)?
To get started
Those relays aren't the best, I've seen a fair share of them go out, apply power and make sure it clicks and applies power to the other side
Alot of those TBI/TPI setups will not fire the fuel pump until it gets the OK from the oil pressure sender - Is that installed and all is well? Usually when they go out they ground out continuously and the pump won't turn OFF so you can still drive, but if it isn't even installed... Who knows what the ECM is thinking?
Those pumps are known to go out - Did you put power to it first and check it?