that is a crappy situation, I`m sure though you can understand, unless whipple themselves did the teardown and inspection after the failure the story could certainly be different. i see it all the time in my job, unless a certified factory trained technician does the repairs, waranty and cost assosiated with the failure are stuck to the customer.
I know warranty claims through the company I work for is a case by case basis, as some components are NOT built in house and giving the customer free replacement may be sticking us in our own foot for the bill, and as for time used for inspection and cleaning (plus travel costs sometimes) its almost never included under warranty. it sucks to use this term in this situation but "It pays to play my friend".
(even though many of the "factory trained techs" I see have little to know experience, its just the way they do things.)
It is great that they sent you a complete new supercharger. hopefully it does not have the same "mysterious" faults as the last one.
I wish you the best of luck with it!
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Lysholm 1600AX, 454ci/7.4L V8. Dynoed at 339hp and 475ft/lbs torque at the wheels. 
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