I'm trying to fit the initial machine entirely within the two top levels, i.e.
Top level - monitor under the glass, + prob a scanline gen in there too
Middle level - controls, xxx in 1 card, power supply & speaker (the power will have to be boxed in to be safe)
Bottom level - will revert to a glass shelf
Its a small coffee table, so the 19" monitor 'just' fits in the top, I can hide its power and VGA cable down one corner leg, each shelf side is around 5-6cm high - not much to play with!
Currently its a stock wired Jamma harness so everything is too long
I was going to box in under the top & middle shelves, but on second thoughts I may try to leave them open to help with ventilation; the only parts that get even warm are the monitor - but no so much if the brightness is low, & the power supply
This pic shows the space under the panel, its 9mm ply with the edge routed back for a flush top; the xxx in 1 is aligned to line up the bolts through the panel & leave enough room for wiring etc - not much space left though:

I have been distracted by having a working machine

It also seems I need something connected to the player 2 cables to adjust settings on the xxx in 1 - a small joypad out of some spare switches will probably work hidden under the main panel.