Universal joints work fine if both shafts are parallel. In this case the output of the transmission will not be parallel to the input of the differential. I don't know how much misalignment you can have before you start to get driveline vibration.

Yes, the 40mm valves are on the large size. Whoever did the work on the head put in large seats and valves, opened up the valve pockets, but did not open up the ports to match. I'm planning on opening up the ports and intake manifold just enough to match up with the Datsun comp manifold gasket. Maybe slightly larger than the GX head but not nearly as crazy as some of the race heads I've seen here and at Dan Hall's shop.