I believe the flywheel has an offset bolt pattern that allows it to be installed one way only.
The whistle/scratch could be a bad throwout bearing, or a busted input shaft bearing retainer if the mechanic forced the tranny on. The pipes might be poorly installed. As far as the stalling, perhaps he disconnected a vacuum line accidentally and it's causing issues, that could affect the brake boost if it was in the right place I suppose.
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