The only solution of number one and two, is to take the rusty metal out, as far back as you can, to good clean workable metal. Then, you make the replacement pieces by carefully bending 20 or 22 guage sheetmetal. You can usually do it piece by piece. Thats how I did my rear wheel wells. They were rotted out, right to the area where the bumper attaches. I cut and butt welded in replacement pieces, along with the inner part of the wheel well.
The hole in the door? Yeah, I remember when I had a nice hole in my passenger door still, same area as yours. I had to replace the rocker panel, and when i put a new rocker panel on, i completly rebuilt the door pillar on the passenger side. Still going strong.
My car has had many close flirtations with death, but I kept it going. Mostly the problems are due to the rot in all 4 wheel wells, both rocker panels, and some door bottoms. Alot of the work is done, but there is still some ahead. I am planning to do more work to it next summer, or continue on into winter while I work at the shop. The most recent work i did was the driver'* side rocker panel. I just cut out the entire panel, from front to rear. Then I put a new repoduction panel, (45 dollars!!) on, welded it in place. Once its painted, it will look good!
Anyways, its all on wheather you have the skill, and equipment to fix this kind of stuff. I have a mig welder, and a gas tank. I also have a shop size air compressor with paint and bodywork tools too. So, to do bodywork on my car, its cheap, compared to the guys who don't have the tools.
Anyways, its all up to you. Sometimes its best to let it go. Maybe you can find a Bonneville, in our years 86-91 that has a much better and workable body. And you could take it, and put a SC 3800 series 2 in it. lol. That'd be fun. Plus, you'd have like others have said, a unique car.