Hey guys,
So I ended up tightening the alternator and AC drive belt some more and I haven't had any squealing whatsoever since, so fingers crossed that problem is dead forever now.
Going back to one of the other main points of this thread - I've been driving with no speakers connected for a while now so that I can listen to the engine noises (trying to spot anything odd). One thing I've noticed is that in the engine bay, there's a whining sound.. very similar to a supercharger winding up/mini-turbo; identical to the whine I would sometimes hear through the speakers.
All I've gathered so far is that it fluctuates loudness/pitch with RPM (same as the speakers) and it's either completely disappearing or it is quiet enough I can't hear it when idling. One thing I was thinking about was that the whine sounds identical to the speaker whine - so maybe this is the source of that issue, and that's why no matter how many times I re-grounded, ran new wires,etc. on the speaker end, I couldn't eliminate it.
I asked on a Facebook page and someone said that they had a similar issue in their Hilux, and it turned out to be their external alternator regulator. Can anyone elaborate on that? Does the MR2 have an internal or external regulator? And would that likely be the issue?
I also read
this article and I feel like maybe troubleshooting the "Circuit causes" section might be worthwhile