I think your idea of temporarily throwing the body onto a bug chassis is a good strategy. I know you were looking to make a “metal jig” to reestablish the body alignment. Towards that goal, nothing is better than the chassis the body was built for. Be careful if there is a lot of rot on the perimeter of the floor pan. You might not be able to trust it entirely. But it’s a sensible starting point.
Regarding engine configuration, obviously do what you want …but (of those options) I’d lean towards a transverse engine/trans like the 4.9 rather than a longitudinal set-up due to the space available. There’s really not enough space even for the transverse 4.9 but there’s really, really, really not enough space for a longitudinal set-up. And mathematically speaking, one “really not enough space” is better than three.
Plus…I’d personally like to see someone play around with the NorthStar (4.9) engine and transaxle. I’ve been quietly developing a new Sterling project for the last two years that has a significantly reconfigured engine compartment (and other neat stuff), and the NorthStar engine/transaxle is one of the top three contenders for drivetrain. (In actuality, I’d like the car to be adaptable to several engines, that being one.)
Going back a few posts, with regards to doors, again do what makes you happy, but don’t give up on the gull wings too quickly. My thought is only this: The coolest thing about these cars is how novel and exotic they look. The crazy canopies and doors contribute to that. Gull wings have a certain cool factor. The canopy has a certain insane quality. (Nobody has done a scissor door on a Cimbria yet to my knowledge. That might be an interesting variant.) Yeah, but normal doors? Those are for Hondas and other practical cars.
As for U-joints and CV joints, I have no direct knowledge. But honestly, I’m not sure they should be mixed and matched. On a CV joint the velocity of rotation is constant throughout a rotation. For a U-joint the rotation of the shaft lurches twice per rotation. If you’re mixing and matching, you’d be asking the shaft itself to absorb those lurches. This might make your shaft unhappy. In general, it’s good to keep one’s shaft happy.