It seems like it might create some unanticipated backpressure and start wearing seals. That's just hypothetical.. Another option I'm considering is just adapting the cobra 96-98 intake manifold right into the C-heads. Any opinions?
Hypothetical is correct. I've researched this enough to tell you any gains on gasket matching is minimal at best. Nothing you would ever see off a dyno and I seriously doubt any concern with 'wearing seals'.
The best exhaust manifold option for full performance would be long tube headers, but it would require a significant amount of custom work.
As for the 96-98 intake manifold adapted to the C-heads, there are better options you could consider. There are several intake manifolds for the C-heads available you could utilize, both OEM and aftermarket. Your better bet would be a 99-01 Cobra intake for the C-heads..