We all have to start somewhere, read up on the consumer law, practice what you are going to say before you walk in. Be firm and polite. Loads of advice on the internet. It sounds like they have pushed you around because you didn't know better. Now is the time to get informed on consumer law. If you are worried about mucking it up, put it clearly in writing and deliver it by hand.
I would start with a tactical acknowledgment that it's not really the shops fault that Cannondale have provided an inadequate wheel(set) and whilst your friends in the shop may have made a bigger hash out of it by doing a bad repair job, it's Cannondales responsibility to sort it. Really, all the shop had to do is trigger the RMA with the manufacturer for warranty claim, however in their defence, this isn't the first port of call, a spoke replacement and true is an easy job, but you've arguably got a duff wheel here that keeps losing tension. You've not damaged the wheel by jamming a tree branch through it (misuse). The wheel needs to be replaced or rebuilt from scratch, the shop has the right to take either course. You can't deal with the manufacturer directly unless the retailer goes bust.
If it does go back to Cannondale, it shouldn't be coming out of the shops pocket, so you don't need to worry about that. Just be polite and firm, don't leave until you've got what you want, they have had their chance to fix the wheel twice and you are back to square one. I suspect up to now, either they were just too lazy to trigger the return, didn't want to lose the bike sale or you haven't impressed on them how poor the wheel actually is. That's the impression you need to make. Don't mention hitting the pothole again, it's practically irrelevant and just gave them an angle to squeeze a repair job out of you! I hope they refunded that btw. If not, demand it once they agree to sort out the warranty claim, as they are then admitting it's a faulty goods issue.
