Pic 3 looks like someone stuck a jack their at some point. Since the jack points on my SD are pretty rusty my dad decided to put the jack on the frame rail. Now with a block of wood to spread the weight this is fine I have done it many times on the SDL when I want a jack stand under the rubber pad. But on the SD it crushed right up into the body!
That thing is a little rusty but I really don't care.
I'd have all of the holes welded up as best as possible. But I wouldn't undercoat the repairs. Undercoating sucks just paint it real good and leave it. That way you can keep and eye on them, just in case they fester again.