I'm in the process of doing the same thing you're facing right now. My car didn't look as bad as yours and I stripped it down to the tub and put it on a rotisserie. I found as I attempted to cut back the rust and replace sections of the damage, that the damage went much further than I could see from the outside. Also, you can't just weld these 19gauge replacement panels to any of that original metal that has any rust on it. The arc even from a quality shielded gas mig welder will be very erratic and produce weak, ineffective welds that won't do you much good in a high stress area like that. I can see from your pictures that most of the floor under that aft spring box area is going to have to come out. that will require you to remove the transmission tunnel floor brace (carefully because this part isn't available). You might be able to use one of those half shut plate repair panels if you can get the old section off and the spring box under it isn't damaged too much. If not you'll have to remove the shock mount braces and cut the whole thing out, locate the proper mounting locations for new spring boxes onto a new shut plate. Have you put any thought into how you want to repair the damaged inner fender where it meets the shut plate? that thing is completely rotted away. How about the inner rocker panel where the shut plate attaches? There has to be a good solid atachment there. All these pieces are made of relatively thin material that when properly joined form a strong structure. but only when all pieces are tightley joined and properly welded. the last thing you want is to get this thing on the road and have the welds start shearing off. Sorry if I sound like a pessimistic know it all, but I see you embarking on the same journey that I started a year and a half ago, and have encountered one demorilizing mess after another! Here's a link to my project. Hope it helps, or that I can be of help in any other way.
Regards
Mark
https://www.spritespot.com/gallery/view_album.php?set_albumName=1960-bugeye-refurb
Regards
Mark
https://www.spritespot.com/gallery/view_album.php?set_albumName=1960-bugeye-refurb