HELP! 3.0 Motor Swap Won't Start

I need help asap! This motor swap has left me without a ride! I saw a thread with the same motor swap, buy can't find it now. So here goes...
I have a 2003 Ford Ranger Edge 2wd with a 3.0. Motor runs great, but I wrecked it last year and it kept eating tires. Then the fuel pump went out. I came across a 1998 Ford Ranger XLT 2wd with a 3.0 with a blown motor, but good body. I thought it would be an easy swap, but BOY WAS I WRONG!
The first problem I encountered was the difference in the motor mounts. A quick trip to the salvage yard fixed that.
The next problem was an alternator difference. I fixed it by pulling my wiring harness from my 2003 and putting it in my 1998. I was just going to rewire it, but the 3rd problem was fixed by pulling the wiring harness. Or so I thought.
The third problem is PATS! The 1998 I have doesn't have it. My 2003 does. So to have right connections and a key I put the engine and dash wiring harnesses and PCM from my 2003 in my 1998. But, it won't start.
I have fire. But, it won't start. What am I missing??? I read something about relearning the PATS when you replace the PCM. Could that be my problem? All I know is I am stranded now and need help to get back rolling! :crying:

UPDATE...Figured out my problem. Firing order! But, found other problems. Will a missing PCV valve cause the motor to run rough? Or could it be a vacuum issue?

Update.... Reset PATS and it cranks and runs. Rough, but I'm adding donor gas tank, fuel pump and sensors. Hopefully that will fix it.

Well, I had it running. Then, started having problems again. PATS is no longer an issue. I am having some sort of fuel pressure issue now.
I have fire. There is fuel in the fuel rail. But, it won't start.