Danny,
1. I would put the Road rage underneath the board. If you use PCB mount pots the board will 'float' in the air a bit. I bet if you're smart you can mount the road rage to the enclosure using some double sided foam tape, and there will probably be enough clearance.
2. Probably yes, but it depends ENTIRELY on where you drill the hole. I recommend you drill carefully and slowly, and only after you have the board and an enclosure in your posession. Actually, a good idea would be to make a fake enclosure from some cereal box cardboard. Make holes in that for the PCB mount pots and then drop the board in there and see what the clearance is like.
3. I'll jump right in and recommend that you use a 125BB. It's exactly the same foot print of the 1590BB but it's about 3/8" taller, meaning that it's got enough clearance for you to not have to worry as much about clearance. You might not have any issues with part heights, or jack locations then. Check it out just to ensure that's true though.
4. 3/8" or 1/4" trimpots are usually the DIY standard. It looks like 1/4" are employed here. I think Mouser is a good bet for those ones.
Jacob