Am I missing something or is this a really long winded process.

If you're in a settlement with the power armor rack there should be a dialogue option for your companion to fix up their stuff using the stores.

It takes ages to get them out of it, position so it's near enough, repair the semi damaged, trade the fully damaged, repair them too, trade it all back and equip.

Anyone got a mod for this yet?

You will need to wait until G.E.C.K. is out to ask for mods. Even if some are out there, the way they are created is harmful for your (save) game.

Fair enough, I assume I'm not missing anything then?

Liking the settlement idea, but I think it could be implemented better particularly where settlers and companions are involved.