On the gear and reforging issue, there's not much you can do about have to reforge each time other than obtain multiple copies of gears and reforge each individually. For spec-specific gear you should look into Outfitter (an addon) to handle the gear swapping automatically (it can trigger off what your activated spec is). Given you're talking about separate PvP and PvE specs, that should be largely separate gear anyway.
The key bindings for the two specs should be being kept by Blizzard, and each time you switch specs you get the key bindings you'd previously set up for that spec. So once you've got them set up how you want them, they should remain as such.
Managing the key bindings instead of just saving them is a bit trickier. I can only often advice and not a definite solution to those - my personal solution is to organize the key bindings by priority basis from 1 across. In PvE, that means my rotation is usually on keys 1 through to 4 or 5, with cooldowns on Shift/Ctrl+1, etc. In PvP, I do similar, with the skills I plan on using a lot (main damage skill, interrupts, CC, etc) on those same keys so that I'm hitting roughly the same keys in both specs.
Power Auras can have their UI triggers edited so that they only appear in certain circumstances. I thought it was triggerable by spec, as I use them for my Paladin to notify me when debuffs drop off my target... which is then pointless for Holy. Unfortunately I'm not 100% on that addon.