So I have several questions now that I'm 55 and getting ready for end-game gear.

My most basic question is this: Will I need to stop wearing the orange shells I have been upgrading this whole time? I got a piece of artifact gear from an oricron mission and found that I couldn't put the armoring from in into another armor piece, is this how all lvl 55 artifact gear works or just a couple of quest rewards?

I ask because I have spent quite a few resources on getting my character's gear to look exactly like they do now, and I would rather keep those shells if possible rather than getting a whole new set of armor.

Also: what is generally considered the best way to gear up? So far I have been running the Black Hole and Section X dailyies and weeklys, but that seems very slow going am I missing something?

You can absolutely keep your orange shells. When you tried to put the armoring in and it didn't work, my guess is that it wasn't for the correct "slot".

Higher level armorings, when removed, will say "Head", "Chest", "Offhand", etc. You won't be able to put a chest armoring into leg gear, for example. As long as you stick to the same type of gear, you'll be fine.

Note that mods and enhancements do not have this restriction. Only armorings, hilts and barrels are restricted this way.

As far as gearing up, here's a guild from Dulfy:

http://dulfy.net/2013/04/14/swtor-level-55-endgame-gearing-guide/