Regarding the stitch welding... Someone more knowledgeable can correct me where I'm wrong, but you shouldn't have welded the strut towers solid to the wheel wells. The reason you stitch weld is so that the metal has some room to flex. Either it flexes... or it cracks. You don't want it to crack. From what I'm gathering you want to use the car for, I wouldn't bother with stitch welding. Just get some bad dog subframe connectors, weld those in, and call it a day.
As for the rust on the rocker, got any pics? Sounds like it's a small spot. If it is, you should be able to cut it out and weld it up and be fine. Keep in mind, there are cars around that were once missing a huge portion of the rocker before it was replaced. Mine, for example, was (still is) missing pretty much the entire top of the rocker from rust.