The empty expansion bay shell (the one that definitely fits the dual m.2 PCB) has a removable back panel, so you can design and 3D-print a panel with mounts for necessary connectors. See the example in another thread. You need to be mindful of the clearance between connectors and the dual m.2 PCB though.
For cooling I’d suggest looking if you could put a slit into the wall of one/both fans so that they expell a bit of air into the expansion bay shell instead of trying to put another fan inside the shell (or dGPU module)