Weld in the Torque boxes first, as they fit better that way. Don't forget to clearance around the spring steel tubing clips so they fit when you need them for your fuel and brake lines.
The hardest part about installing the SFC's is trimming them to fit correctly. Patience & more patience is the key. They are not an easy fit.
Don't forget to cut a notch in the passenger side SFC for the fuel lines, where the SFC meets the frame cross member.
The Parking Brake Cable on the driver side is another issue.
We make 2 offset elongated notches in the SFC so the cable runs correctly along the bottom of the floor pan and doesn't have to go over the SFC. It will work going over but doesn't look clean and correct.
We also cut 1 more elongated drain hole in each SFC, to match the 2 existing holes already in the bottom of the SFC's, to assist in the priming/painting process. 3 identical holes spaced correctly looks great.
Always use weld thru primer on any overlapping metal joint..
As for priming/paint protecting inside the boxes or SFC's, do it after welding because of all the heat. You can paint some of the inside before welding in, but you have to stay away from where you'll weld next. I have done it both ways. Your choice. Eastwood has different 2K spray cans just for this application. And you will be able to use their plastic spray hose extension, to get inside the frame or torque boxes. It really helps if you put a stiff wire like a coat hanger inside the plastic hose extension, that way it will stay straight & then you can bend it to spray at any angle when necessary.
And lastly, I hope you are doing this on a rotisserie, as doing this overhead would be a pain...
Good luck.