I've seemingly gone full circle again and it hasn't gotten any smarter.
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I got a call back from BoostedTech and they don't see anything wrong with the supercharger. After I specifically told him to rotate the rotors and look at the damage (pictured in previous posts) he said that he did see one little divot that isn't a problem and can be filed off.
He said that he can't feel any issues rotating it by hand and in fact it feels like one of the best units they've had.
He isn't going to open it, and is not able to test it on an engine under the conditions the issue happens under, he is not sure that the rotors are or are not deflecting under load because he can not test it, he has no further diagnoses to do. In his conclusion there is nothing wrong with the supercharger and is ready to send it back.
He said that the issue is probably a vacuum leak in the engine intake (around the TB) or exhaust. There are no leaks that can be found in a shop on my engine. He did not know how to test these with the engine running under the conditions that the issue occurs.
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It seems that my options are still a bad supercharger, bad engine, or bad transmission and the only way to feasibly test them is to either 1) throw parts at the problem and fully rebuild each, or 2) swap around different supercharger, engine, transmission combos until I narrow down which is the problem. Both of these are incredibly expensive and time consuming ways to deal with the problem.
Any ideas?