Are you still driving the car with the blown turbo? It's entirely possible you're starting to get pieces of metal from the turbo into your engine and you're destroying it. It's also entirely possible your cat in your UP has come apart from running stage 2, and maybe also from having pieces of your turbo get into it, so that has gotten into your engine too.
You need to stop driving your car and take the turbo and UP off to see if you've wrecked your engine and not just your turbo.
It isn't really going to be good for your karma to put a turbo with 100k miles on it in there so you're giving somebody else your problems. Personally that would really bother my conscience, but maybe you're ok with it.
You can save yourself some money by just gutting you stock UP instead of spending hundreds on the Cobb part or somebody else's aftermarket one. In 20 minutes with a long screwdriver and a hammer you can gut your stocker. If you look around you should be able to find a low mileage OEM turbo to save yourself some money too. If the shop is unwilling to warranty parts they install I'd go somewhere else. Any reputable shop will warranty parts and repairs for at least 30 days, though it's not unusual for a shop to not warranty a used part. Where would they be sourcing the used turbo from?
What you should do really depends a lot on your financial situation. If you really don't want to get a new payment, and you really love your car, then it sounds like your decision is already made: Fix your car and drive it.