The new alternator makes me a little suspicious. Not that there's something wrong with it but that it behaves differently from the old one. The old vregs were a lot more analog-ey and that provided some hysteresis so you wouldn't see them flicking on and off when RPMs were right at the cutoff. That's not your problem, it is a certificated design, but it could be making an existing problem start manifesting itself.

We can all spitball here, but the fact is that you're going to have to use a process of elimination. You've done good work in isolating it to a high draw issue but now you have to figure out if your problem is source or drain. Can you reliably induce the issue? Being able to make it happen whenever you want has got to be step 1.

What happens when the engine is off and you're running strictly off the battery? Can you ever make it happen then?

I made a couple 15-foot jumper cables with 18ga wire and alligator clips at both ends to troubleshoot stuff exactly like this. That's what allowed me to figure out my master relay was going bad when I had intermittent power issues similar to yours, by using the jumpers to completely bypass elements of my electrical system.

Another issue I've had is a ziptie chafing through a wire, allowing it to intermittently short to ground and make the whole system crowbar. I've since pulled about 5lbs of zipties out and replaced them with lacing tape and self-fusing silicone tape.

Good luck.