Hey Jross14, Welcome to AF. You'll get a better response to your problem if you start a new thread...this one was 4 years old. Questions to answer in your new thread:
Did the problem start suddenly, right after the engine install, or gradually? How many miiles? Manual or auto transmission? Ever had any problems starting, or if auto, any weird shifting issues?
My first reaction, without those answers, is to think it's either the Neutral Safety Switch (NSS) or the Crankshaft Position Sensor (CPS), but both of those are mounted on the transmission.
Please start a new thread and we'll go from there.
Thanks.