Intake/exhaust manifold nut trouble

That's just odd. I've never needed anything more than straight extensions and regular sockets to get the deed done on a slant.
The bolt clearances change when Clifford Intakes, Dutra Exhausts and wrapped headers are put into the mix. Some of the bolt clearance goes away.
I have never done it, but I would think that installing a Hyper Pac intake in chassis would be a pain.