Warpage from welds: I would suggest, where you can access the weld site, that you do a few tacks and then while the metal is still a bit warm, use a hammer and dolly to tap on the welds to stretch them out a bit. You see, as the weld which fills the gap between your panels cools, it shrinks and this is what causes the warp - the more welds, the more warp.
Looking at some of your repairs, first of all kudos for taking the job on. Nothing like getting your hands dirty and making your way up a learning curve.
I would say you are erring too much on the side of caution and that many of the patches you are cutting out are too small. Making fiddly small patches in the interests of minimal disturbance of the surrounding sheet metal increases the work and it's difficulty, and leads to poorer results generally. It looks to me like you're not getting at the rust underneath properly. Some of the welds look contaminated - not enough surface prep, inside and out. You want to look on the inside of the panel and make sure you have cut out all the rusty metal - or at least get the metal free of all rut before welding in a patch. You can't rely on the coatings and herculiner, etc, to do anything but conceal the rust and let it spread without your notice. You've gotta get all the rust out before doing the repair.
In some cases it would make more sense to drill out the spotwelds between pieces so as to separate them completely, then media blast the metal, then repair the pieces while you can get at them more completely, reassemble and weld - then treat with a corrosion-inhibiting primer. Otherwise I see a lot of places where that rust is just going to come right back. Grinding cutting and welding is a lot of messy dangerous work and take it from me, it is disheartening to see the rust coming back a couple of years down the line after all the time trouble and expense.
An experienced bodywork guy told me, when I was wrapping up the work on my truck, that "you'll probably have to do it twice over before it comes out the way you want it". He was right.