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.