i don't know much about pre 5th gen civics but alot of times there is a heat sheild hooked onto the exhaust pipe right below the shift linkage because the heat sheild can't be bolted to the car in that spot. i just put a short shifter in my car today and i removed that portion of the heat sheild and there is plently of clearance even though it is a stock exhaust.
otherwise you could get new rubber hangers like others said or just try to bend the metal hangers a bit to lower the pipe a centemetr or two
i don't know how hard that would be but it's a thought
good luck
Sean
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