Checking the charging system at Advanced may have shown that voltage was
getting to the battery, but doesn't mean the sytem is operating properly.
I don't know how they checked it either. There are two connectors to the alt.
One goes to the battery, the other, PCM. I'd be checking these wires for any
breaks or loose connections at this plug.

Of the three wires, 2 Yellow/Lt Blue and Yellow, go to the PCM, the Orange/ Lt Blue
go to your fuse box #43 10a, listed as alternator in the manual.
I'd check these areas before changing alts and PCM work.
You've got nothing to lose......