Well, Rex beat me to suggesting the notion of having an anti-crush bushing or block for the bolts in the rear frame bolted joints. But beyond that, I would be rather leery of that style connection in the first place--too much difficulty with alignment, tolerances, interface fitment, corrosion, and wear. Some sort of flanged connection would seem to be simpler, more robust, and easier to live with.
Am waiting to see what you have in mind for the rear frame to control what, at this point, looks to be very limber in roll rotation.
With you in the frame, there appears to be little space for the pedal arrangement.
Front suspension sub-frame is, again, BOLTED(?) to the main frame? Using thinwall tubular members?
Could you show an example of the CAD drawing of a tube element as would be needed for laser cutting?