Not sure where you are with this, but once my 95 Millenia 2.5 wouldnt' shut off. Discovered that while checking fuses under the dashboard, I'd inadvertently put one of the fuses back in the wrong spot. Car wouldn't turn off. Days later, I remembered that I'd been monkeying with the fuses and tried changing them around. That fixed it and car shut down normally.
About to do an alternator change out on my 200k Millenia tomorrow. Good luck.
1995 Millenia 2.5L