Re: stack orientation
If you're going to use an open stack (I wouldn't) a stack with its axis 90° to the wheelbase will have a slight siphoning effect as speed increases that will change the mixture slightly. I have a feeling that it's not linear though, but has minimal effect below X mph, and a sharp increase - but what "X" is IKBA.
A forward stack (although obviously a dust, small bird etc. vacuum) will only experience a slight pressure increase as speed goes up, but as long as the air correct is inside the stack it's harmless.
My choice is the surround a 90° stack with a large volume air box ending in a sized forward entry. Near side of the box is flat, and sandwiched between the carburetor body and the stack flanges.
Remember that any jetting you develop will need serious tweaks for elevation.
Looks like you have more than 1 Thunderjet in there? Not to confuse you but if there are more than one they need not be mounted at the same distance from the throttle shaft, not at the same depth from the wall, and not the same jets sizes, etc. In general, the farther from the wall the earlier it adds mixture in the RPM range.
If after lengthy testing you have a flat spot that you can't get rid of, I would consider making the primary length adjustable since you've nicely made them parallel (you can buy swedged short pieces, just cut-n-insert). Remember your tuned length will be different at the salt due to air density, air temp, etc. anyway.
If you get to this point, the final position of the collector can be moved a bit. It won't affect the tuning, but angling the collector up so that the exhaust aligns with the trailing edge of your aero shape (probably your gluteus maximus), and inward to the tire centerline reduces your drag somewhat. If you do the math first, you can rotate the collector on the stub and angle it up and in with 1 cut (although I would prefer a 3" radius bend here).
As was stated, I don't think your frame is stiff enough (no comments!) - I don't mean it will break, I mean it may not be as stable as possible given the geometry. Much of the general design doesn't lend itself to easy changes, but 2 pieces easily made with your notcher will improve an obvious weak link: the drive side. Here's the idea:
The angles need adjustment. The vertical evenly divides the span lengths of the 2 rails, and the horizontal goes from mid-height back to the axle plate. Same OD/ID as frame.
As used on H-D factory race bikes as far back as 1928.
