This is the kind of situation where you pull a refund scam and it's okay because you're not really scamming anyone - it's just a free extended warranty plan. But a completely new Xbox 360 at the full price from a place like Target or Wal-mart. Then swap out the innards and return the old broken Xbox in the new Xbox case. There are tutorials on Google/Youtube that will show you how to disassemble an Xbox 360.
As long as you don't mess up the casing of the Xbox, there's really no way for them to tell that you're returning a broken Xbox. Even if you do mess up the casing, most employees won't notice. They only check to make sure everything is in the box. When they ask for the reason you're returning it, say because it's broken. This way it will go back to Microsoft and not back on the shelf. If they ask if you'd like to replace it for another one, tell them no because you already bought a new one from Best Buy.
I hope you can get that $99 back and do it my way instead. You shouldn't have to pay to service these things. They should just work since you paid several hundred dollars for it in the first place.