2007 Yaris S alternator overcharged battery, replaced both now no P/S

[Ala2014]

My car's Christmas present to me was to die during my drive home for the holiday. I had been having odd issue with seeing Battery light, SRS airbag light and P/S warning light come on and off and on again for a few weeks now, and no one could figure out what the issue was - battery and alternator kept checking out fine when I would stop and have them checked at AutoZone. And no codes were coming through on their code reader.

When it died, we finally realized the issue as it was clear the battery boiled over, and I could definitely smell the hydrogen sulfate that I've heard comes with this issue.

So here's what's been fixed/replaced:
battery
alternator
headlights (high beams were fine)
taillights
turning signal bulbs
fuse for horn

We (ok, my dad) has checked all the fuses (under the hood, on the positive battery terminal, and at the driver's foot under the dash) and they all make a beep on his voltmeter. We even had a friend with an intelligent tester check things out, and it came back that there was a communication error.

Current problem: P/S light on, no power steering assist, INT wiper doesn't work but lo/hi do, and driver side door window won't go down but other 3 will just fine. Car is running fine otherwise - no other dash lights on, and all other functions check out ok (cruise, radio, fog lights, etc).

Searched the forum to see what everyone was saying about P/S issues. Found that next we should probably check the DTCs manually. Wondered if anyone would like to offer other advice.

Thanks in advance! Crossing my fingers it's something we missed or an easy fix.

-April