Good on you for trying to save this beast. You need to move out of the salt. Nevada, California, Arizona, maybe New Mexico.
Frame rust would make me crazy, so good work and keep going.
As an aside, have you removed the vinyl covers over the rear wheel arches? Even here in California I've had some rust spots inside the rear wheel arches on the vertical surface. The PO took it to Lake Tahoe to ski and that was enough. It's normally covered, so you have to look for it.
Rust is evil. It's entropy. You have to keep applying energy just to keep up with it.
Rust is inevitable in these vehicles. Living anywhere that they treat the roads (salt is not the worse they use these days) it will creep in and eat exposed metal
That said there are ways to protect metal. Oiling the chassis, using things like fluid film/ Waxoyl in the corners of the body, etc.
While you cannot get everywhere (some cases due to heat) anyplace helps.
My rig grew up in Chicago area, then moved to Rhode Island and finally to New Hampshire. None of these are great places for rust.
The PO oiled the chassis and also did the rear wheel wells (much later) . The chassis held up and is actually looking great. Some minor lifting at the C Channels, but nothing that I need to address any time soon. The upper shock mount broke and was replaced, aside from that places that were not treated rusted out (heater tubes, mounts for heat shields)
The wheel wells as they were done late, needed some work but now are back to their former glory and will be sprayed on the inside with Fluid film as will everywhere else I can get it in.
So Rust sucks, but how we deal with it in the East is what matters. Ignore it and there will be nothing left. Treat it and the vehicle will last for years.
Patching the panels and rebuilding part of the frame is fine. You HAVE to spray the heck out of it when done to protect it.
Heck is if a 45 year+ old Land Rover can survive with just using Waxoyl then our Cruisers will be fine.
For those that do not know old Land Rover frames are made of Tin I swear.