I had a similarly confusing situation this year when I bought new gear for the first time in years. I mean 10 years. The first day out as brutal on my feet, but I ignored it thinking it would go away as the boots wore in.
turns out I was simply doing the boots up too tight. sounds stupid right?
if I did the boot liner up snug, but not as tight as possible (as I had been doing at first), and then proceeded to do up the boots, my feet were fine.
on the off chance this solves your issue (unlikely, since you've already tried so many things) or helps someone else in a similar situation, I'll put it out there. don't do the liners up so tight, but keep the outers tight. see if that works.