Post a pic of the bolt sticking out, then we'd be able to answer your question better. It might be a bracket mount, but can't really answer till I see it.
As for your main problem, replace all you vacuum lines or at the very least, check them all for cracks. You might have one clogged on the inside though so changing them out is your best bet.
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1989 N/A Targa 5spd. Metallic Grey, w/grey interior. No mods done.
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