Hello, Aaron.
I don't have a 292 or (250, 230, etc).
But I have seen several threads on changing the inake and / or the exhaust.
Do the tie bars (the plates that go over the bolts or studs to clamp on both the intake and exhaust at the same time) sit level under the nut / bolt head (I don't know if you have studs or bolts on yours)?
I've seen that mentioned as causing a problem if it's not. I've seen both grinding (within reason) and shimming under the tie bar used as a solution for differing flange thicknesses.
Hope that helps.
Those that know more about this will likely want to know which aluminum intake (Clifford, Offy, somone elses ???) and who made the header/s also if they are tube headers or cast headers (aka 'split manifolds' or 'dumps').