Thanks for the clarifying questions!
Yes, bundles need to stand on their own, so a 2 or joker or red 3 used in one bundle cannot also be used in another bundle.
Because red 3’s don’t have a “rank” unto themselves apart from being in a bundle, you wouldn’t have to discard one if you got a bad bomb. When I play, I have a separate pile for all of my wilds, and wait to add them to my bundles at the very end. You could choose to add your wilds to a bundle at any time though, or even move from one bundle to another, as long as again you only use each wild once.