Ok so about a month ago I put in a preorder to Gamestop for the regular edition of STO. I didn't preorder the Collector's edition at the time in part because there was some confusion over what uniforms came with it, (turns out the ones I wanted only come with the Collector's ed.). I am still waiting on my game from Gamestop but now have a little extra money and wouldn't mind getting the collector's edition instead. What I'm thinking of doing is when my game arrives taking it to the Gamestop store in the next town and get a refund and/or exchange it for the collector's edition. My question, if anyone happens to know, is if I were to do this would I lose out on the pre-order bonus or would I still get it since I'd still be putting in a retail code from a copy of the game from Gamestop?

The bonuses are linked to the retail key you enter in. If you enter in a Gamestop key for the CE, you will get those on top of anything else you might have already linked. You shouldn't lose anything. Good luck getting a copy of the CE though. For a game like this, it is quite likely that Gamestop was only sent a few copies to sell that weren't preordered, if any.