What motor does this have in it? EFI I am guessing? It could be the MAF sensor (Mass Air Flow). Typically when a fuel injected vehicle first starts up it will run in open loop, which means it runs on a pre-determined set of values for fuel ratio. Once the motor heats up it will start reading the O2 sensor and MAF sensor and others (Temp, Manifold pressure, ect...) and then begin adjusting the amount of fuel into the motor based on these values. If the O2 sensor / MAF or other sensor is bad it can get some false readings and either starve the motor or flood the motor. Either way, it can fall on its face.
A "no start" along with the other problems you described seems more like a fuel delivery problem or the motor is getting flooded. Maybe Plugged fuel pump/fuel line, bad ground preventing pump from running correctly, fuel pump relay problem, the list goes on and on.
Was you ever able to pull the trouble codes? What where they?
Here are some DTC info I pulled up real quick that should be able to help you down the right path. Also the How to read the DTC PDF.
Good luck. It can be frustrating, but your building a pretty sweet rig. Keep up the good work. I'll be watching this build as it progresses.