Making everyone happy with a custom frame is a tough job.
Change too much and nothing stock fits.
The backbone tail section should accept stock and aftermarket tanks and tail sections (sohc specific), for simplicity.
But in a cafe I would see a frame with twin shocks still, longer swingarm, boxed, rearset mounts, mounts/tabs for buddy pegs or exhaust hangers, oil cooler mount tabs, adjustable steering lock and maybe eccentric headstock for steering angle changes including triple clamps which provide more width for a wider wheel setup.
Mounts or tabs could be just threaded bosses in the frame so they wouldn't be so unsightly if not used.
A trellis frame will make for a wide frame. Mono shock will make for a long bike as the motor/tranny is long and not compact as todays motors are. An overhead monoshock could shorten things up a bit, but there wouldn't be room for both the airbox/electrics and shock.
A stock styled frame, braced where they are braced now (for roadracing) with flush mounts/tabs would be the most cost effective.
Bimota kit style comes to mind... Parts or roller.
Not cheap in todays market!
Look at TTR stuff. Beautiful, but not cheap.
