Here's some stuff I noted down in case it's helpful for anyone else:
- The random white square with the slot in it is for when you mount an expansion card; it goes on the outside when you do.
- Board first, then power/reset buttons.
- The Pico-ATX power supply is right up against the side, and the cables butt against the side of the case, so you'll need to be comfortable with bending them around. I unplugged the Molex cables too.
- On my faceplate, the backside is just glossy and I don't think there's a peel-off on it. At least, that's what I'm telling myself after spending 20 minutes on it.
- The VERA shifts around when you plug cables into it, so be gentle. I dunno if it's just my board or if this is just how it is. I didn't notice before because I'd hold the VERA to plug cables into it, which you can't do when the board's in the case.
- My bottom plate came with all of the standoffs pre-installed, and it would probably have been a good idea to check that they were all in securely before mounting the board. They're probably fine, I just didn't think to do it. (EDIT: I've since checked, they were rock-solid, so there was nothing to worry about!)
- Purple plate gang represent.
- Power button on the right gang represent.
- Definitely didn't drop a screw onto the carpet gang represent.
The final thing I would be looking for is, a really nice Commander X16 badge to put on the front, one that's nice and silvery and with the rainbow logo on it.