You have 4 unnecessary steps.
1) Remove gear-based PvP.
The end. This pretty much solves all of the other issues you listed. PvP doesn't need to be a completely separate gear grind. It's just another MMO time sink that forces players who want to enjoy both aspects of the game to grind out another set of gear.
Allow players to use whatever moddable shell they want, and have armorings/mods available for purchase so that players can customize stats to their liking with reasonable thresholds in mind. Tanks should be able to mod for higher HP, while DPS should be able to mod for higher damage. Put Alacrity stats on healer gear so that it actually means something.
Keep the token system for unique PvP moddable armor shells for aesthetics only! Level the playing field.
Yep. That's why quite a few people don't even do pvp right there. And here I thought they weren't trying to make pvp feel like a separate game.