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i've had boost brothers headers on my car for bout a year...and the linkage rubs but its really not bad now. i just wanted to get the engine raised slightly so they wouldnt rub at all.
I put prothanes on about 2 years ago and they DEFINITELY lowered my motor about a 1/4 inch. Did they change their design?
The standard mounts raise it 1/4-1/2". I had to rework my JLTII to get it off the hood liner after the mounts even without all the engine movement the stock mounts had.
The ones sold for supercharged cars have the aluminum "puck" cut to increase hood clearance.
Sounds like you have the supercharger mounts.
PS with the design of the Prothane Mounts is may be possible to cut spacers to adjust mount height.