Hi Rick and welcome!
Your build looks very nice. I am going to blow through these questions really quick because I am doing a lot of running today. If I miss something or someone wants to embellish please do.
- Yes. BO is Board Out and BI is Board In.
- Yes. It is a six and one/half dozen kind of deal or ham and mustard vs. mustard and ham.
- Yes. If you flip it the other color will be the On color. You can test this easily with a 3 to 5v coin battery.
- Yes on the Pots. It is another six and one/half deal since many would wire pots through the top and fold the pots over when installing to the enclosure. No rights or wrongs. This is one of our first from over 10 years ago and we were still figuring out our standards.
- You can socket that area if you like. It will not work without that resistor in the circuit. The standard value we have I feel is a good value for most guitars until you enter high output territory. Over 10k.
I hope that helps. Sorry for being in a rush but I think I covered everything.
Here is the link to our Guides Page if you have other questions on this or future builds.
Here for convenience below are two charts take from the Guides Page.