happy to help mate.
i use 1.2mm thick steel for the floor/jacking point areas. it's about as thick as can be shaped although it's pretty tough doing so, and can be cut using hand tin-snips, just! makes a better job as it's pretty strong stuff. i would reccomend bracing the inside above the jackign point like i have done on this sud, every little bit helps to stiffen up the struncture and make sure you can you the jacking points in safety
the weldable primers are ok for the sections you close in although as you say, they do actually hinder a good weld i find. if you use them it pays to clean off the area where you weld, so pointless really getting the weldable stuff. just my opinion.
i spray the inner faces with a zinc primer or red oxide. once it's closed in you can still give it a good dose from inside the car through the holes in the inner sill, get a good mist going. doesn't matter if it runs out the bottom, more is better than less. once the welding is complete then waxoyl or similar can be sprayed into the cavities, that will keep it rust free for the future.
the holes for the plug welds on the bottom lip i space about 3" or 4" apart, more closely near the ends. the holes can be punched in by a joggler that has the reversing hole punch but i find them not big enough. i drill holes about 8mm diameter, that allows a decent weld pool to build up thus making for a stronger weld than with the small holes the hole punch makes.
you may find you need to make a new lip for the sill to be welded to, if it's rusted then it won't weld well at all. the weld will spit & spread out, easy to disguise something as being welded so the mot man is happy but no strength to it. making a new sill lip isn't too hard and will make a longer lasting job of it.
we all start somewhere, practice improves things. i'm just happy that what i do is inspirational