I do mine just like that out of the box! Except I only soldier one leg of each pot. The pots have more give to them that way when installing it all in the box. Then once everything is done, I soldier the last two legs of each pot. No more struggling with getting all the shafts in the holes!
I need to find the video that showed the technique I currently use. It's way better than what I used to do. Basically:
1. Populate the board without the LED, lead wires, or pots.
2. Drill the enclosure
3. Bend pot lugs so that they make a "\ | /" shape. This creates tension and makes them not fall out when you put em in the board...and do that.
4. *
KEY STEP* Place the board with pots in your enclosure holes, loosely snug them in with the nuts. Press board all the way til it stops against the pot legs then lift each side of the PCB up a hair to create a 1mm gap between it and the pot "leg-stops". This is insurance against pot cover grounding issues.
5. Solder the pots in now. This makes it so that everything slides in nice and easy when the time comes for final assembly.
6. Remove board (now with pots) from enclosure then solder in the lead wires on the north edge of the board, wire in the footswitch, then the in/out jack's.
7. Tighten a DC jack into the empty enclosure and add LED bezel now, if using.
8. Place entire circuit assembly back into the enclosure. Test fit your LED and solder it in.
9. Solder the last leads to the DC jack then tighten everything else down.
10. Pray everything works.