Good Evening;
Need help understanding why my exchange of engine is not working.
Had a blown 3.0 2001 auto.
Installed a 1999 4.0 / (push rod )/ auto ,wiring harness(engine) & PCM from donor ,had PCM "flashed"at dealer
The key would not start truck (jumped the relay ,now starts),charging system would not charge( jumped relay,now charging )
Some idiot lights are still on,Tranny shifting hard , .O.D. light is blinking on dash .etc...
the question is ... what am I missing ?

All connectors plugged together _ different ?
PATS ?
new program needed ?
?
Thanks ...

 

2001 would have PATS type E
1999 PATS type B

Type E had PATS in the PCM

I think PATS type B had a separate PATS module above the glove box that was "married" to the PCM.
So you would need both units.
I didn't think you could "flash" Type B unless it was in the vehicle with separate PATS module connected.

What is the Anti-theft light doing?
It should flash a couple of times when key is turned on, and if key passes the PATS test then light will go off, if it continues to flash then you have a PATS issue.

But that would only effect starter motor and/or fuel system, that is all that PATS controlled.
It wouldn't explain the alternator charge issue.

2001 might be using "smart charging" and '99 didn't so there would be a wiring difference.

I would say this will not be a simple fix.

What "idiot lights" are still on?

You should probably get/rent a scanner/reader and see what codes the computer(PCM) has in memory, then address them one at a time, and remember codes usually mean Sensors are GOOD, and are reporting a problem, so don't shoot the messenger.