Check your linkage. It sounds like something got bent. If it worked before you took it apart, then it's highly unlikely either the carb base plate or manifold got warped. You didn't say where the blue rtv came from. Also, why did you take it apart in the first place?? What was the problem??
At any rate, what you describe would have to entail some major distortion of either component (not likely), unless you did something nasty when you reassembled it.

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Jeff L
1987 300e
1989 300e
1987 BMW 325