Basically played horde in the expansion until now and decided to play my alliance rogue since I ran out of stuff to do on my DK, if I stay on my alliance rogue when 8.2 goes live and complete pathfinder part 2 on him, will that still unlock flying.
I would expect so, since as far as I can tell Pathfinder Part 1 is the same achievement for both horde and alliance (it has dependencies that can be one or the other, but Pathfinder1 itself seems to be universal). But I could be mistaken =/
Or… if I finished Pathfinder 1 on my druid, but then decide to switch mains to my hunter, can I get Pathfinder 2 on my hunter and get flying?
Yes this is no problem at all. If you look at the Pathfinder 2 achievement on your hunter (or even your Shaman you posted on) you will see it already has check marks for PF 1, and the two new Explore achieves. This is how account-wide achieves work. So if you now grind the two reps to Revered on your hunter (or any other character or even one on each), the account wide achieve will fill in and you will finish PF 2.