Frame rail options

I would replace the rails. With rust you have to figure there's twice as much there as what you've already seen, and that's on the conservative side. Based on what you described I wouldn't try to patch them, it will be a lot more work. You'll have to find donors because as of right now the rails aren't reproduced. Crackedback or whitepunkonitro might be able to help, shipping the rails isn't actually that bad.