Lots of good questions.

Getting a lid and cutting holes for net pots is great. You'd fill the net pots with hydroton, and the bottom of the tray should be empty. No hydroton. Your nutes will fill it and drain and the roots will just be free in there.

You can put rooter plugs in rockwool, but there is no need. I'm not a fan and since you'd be using netpots you would just put your plugs directly into the net pot and fill it with hydroton. NEVER rip open the plug once its been rooted.

In a 3X space I would grow between 1 and 4 plants. 1 would be huge, but you run the risk of losing your whole crop too easily. Pretty much no matter how many plants you run you will yield the same total.