After I test fitted the inner rocker and torque box as an assembly, I marked each for it's relative position against the outer rocker and front floor support. I removed them and then drilled umpteen-bazillion holes (okay, I'm exaggerating a little) along the top and bottom of the inner rocker every 2 inches as wells as in strategic locations around the torque box. The rear 1.5" feet or so of the top flange of the inner rocker had to be drilled instead of the outer rocker because of the inaccessibility of the upper flange due to the rear quarter panel and rear door support structures. I also drilled the outside edge of the bottom of the rear torque box to be welded up against the bottom of the inner rocker.
After having drilled all those holes, I reinstalled the panels into the car and clamped them back in place. I then marked each hole's position on the panel behind it with the tip of a sharpie as you can see from the front torque box area here:
... and along the outer rocker here:
I then removed the panels... again... and used a flat-end spot weld drill to expose bare metal under each sharpie dot to weld to. This is a royal pain compared to just spraying weld-through primer on and welding through it but my theory is that welding to bare metal splatters less and is easier to do than into weld-through primers and the bar metal is protected with PPG primer all the way up to the actual plug weld itself with no bare metal exposed between panels. Frankly, I don't trust weld-through primer to protect the metal as good as PPG primer and/or ZeroRust can. My Ford Weld & Sealant Assembly Manual called for weld-through primer between panels and look how well that worked out!
Here's a shot of the rear section of the inner rocker where it attaches to the rear torque box and outer rocker. This area required welds along the edges of the rear spring perch, the top flange of the inner rocker, and the outside edge of the rear torque box bottom where it contacts the bottom of the inner rocker. Note the color differences between PPG's DP74LF primer (the rocker panel), and ZeroRust Red Oxide (the other stuff).
Looking forward to the front torque box. Welds required along the torque box to inner rocker flanges, the cowl side panel, side and bottom of the floor support:
A seam weld was required along the frame rail with welds to the inner rocker end flange, the bottom outside section of the torque box to the bottom of the inner rocker, the bottom of the frame rail/floor support and, of course, all along the bottom and top of the outer rocker: