Engine 2002 3.8, Replaced Motor. Cranks But Won't Start

I just recently bought a replacement motor for my 2002 3.8l, the salvage yard had run it and compression tested it and claims it is a good one. It has a warranty.

The motor is in, and thanks to some fine posts here in Stangnet I was able to diagnose the first problem of my "no start" condition... A bad fuel pump. I have replaced it and it is priming and building fuel pressure.

Now I have spark and fuel pressure... But still no start. It cranks over just fine but not even a hint of firing. I am at a stand still again.

I must be overlooking something:
- All electrical is connected, I have spark
- I replaced the fuel pump and filter and there is fuel pressure
- I put a new serpentine belt on it
- Everything is connected and bolted up except the exhaust

Any trouble shooting tips would be greatly appreciated,

Thanks,
 
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So, got up this morning and tried to start it, and it fired up. I hooked up the exhaust and after a rough patch it smoothed out. I ran some injector cleaner through it and now it runs like a champ.

Now I have another issue, I filled the transmission with Mercon LV but the transmission will not engage. I let it warm up shifted it into Reverse and Drive and nothing. Everything is is connected, no blown fuses.

Will post another thread for that.

Joe