'running ragged' could mean any combination of things. Do your best, if you haven't already, to recover the entire shop towel to see if you can account for most/all of it. No telling what path the towel took if it was torn up. Could have gone straight into the intake manifold and engine, or taken a ride thru the supercharger.
I'd pull the belt off the supercharger and see how it spins by hand - easy enough to do, just swing the tensioner and drop the belt at the SC. If it complains, I'd be tempted to remove the supercharger top so I could inspect the rotors. If the towel made it past the supercharger, bits could be plugging the intercooler, so if that seems likely, you may want to yank it and look inside.
Not sure I'd run it again until I knew more about what's going on internally. Might need to pull the plugs and do a compression test to see if any valves are bent/stuck open. Not easy to do, but with the plugs out, you could use an inspection camera to check the valves, etc.
If you can account for the whole towel, tho, might just be it's not happy from sitting
(plugs/wires) and/or you've got some whacking good vacuum leaks....if the intercooler tubes were loose, do you know what the process was to re-seal them on assembly? They can be a chore to get sealed again, and if they leak, the engine will run ragged, for sure...ask me how I know
Fingers crossed that's all that's wrong.
Remember, an alternative to firing the engine after dealing with vacuum leaks is to smoke test it.
Tough one...good luck.
Ken