I found some good high res internal pics and it looks like a CEB motherboard should fit with a few modifications.
1) The rail that suspends the 120mm fans will have to be moved back towards the drive bays to accommodate the extra 1" of motherboard.
2) I'll probably have to drill an additional row of holes to support the edge of the motherboard. There will be a solid 1" overlap from the last screw hole and this happens to be the heaviest part of the board too. Plastic standoffs will probably work OK for this.
That should be about it. Luckily CEB isn't too huge. If I had bought the 5100x board I was looking at I would probably need a legitimate E-ATX case.
I also found a case that looks somewhat similar to the old NeXT Cube in terms of front panel design. That might be fun too. I'd have to find a vintage NeXT case badge.