I spoke to the shop. I am going to hold off on the re-clearing for now. They do a chemical strip and then 3 coats of clear-coat. If there are pinholes, they will sand it down by hand then re-clear it for no extra cost. They have done carbon parts before and guarantee a lifetime warranty on all their paint jobs. To their knowledge, hand sanding it has fixed remaining issues with bubbles. Also, they said there is no "tinted" clear coat, but they can do a mix of the black and clear which gives it a smoked look. I was not so sure about this, but I let it go since I was holding off anyway.
Thanks for the info. I'll repost on here if I ever decide to do it. Depending on the contrast between my old and new carbon parts, I may end up having to do it anyway.