Most of the plug welds and fused welds will be fairly evident. There are several ways to deal with plugs. Harbor Freight offers a micro belt sander that can be used to clean and expose the weld points. After that you can take the time and use a center punch to dimple the approximate center of each weld.
Despite the PR flak, the self centering plug weld drills/cutters don't really self center without a lot of effort or in the absence of the center punch dimple. They will tend to walk or skitter around and the spring loaded centering pin can jam or get dull or even break; same/same with the drill bits. The whole point of cutting the weld is to just cut the top layer and not drill through.
On that note, Steck makes a seam splitter than you can use to get under the seams between the welds and lift them up so the splitter can chisel them away. That leaves you with the plugs which you can then whittle down using a flap wheel on a 4.5 mini grinder. For tight spots that micro belt sander can get in where the grinder can't.
I also agree that that one area on the inner wall of the drivers side does look rather cancerous even if there are no holes. The degree and depth of the acne means that you can never get it all clean and free from rust, which in turn means that any MIG work you do will may have the side effect of causing blow throughs in the deteriorated areas.
Anyway you elect to go about it, do be aware that the labor involved is time consuming and tedious; and necessary if you want to end up with a product that is strong and which will last.
Nick