I just wanted to thank everyone so much for all their help! I would have said so earlier but just got back from a week long trip with no wifi/ cellular. It took a few times of loading and saving in game and saving using pokemon chest and pkhex but everything seems to be working!
Ultimately only 4 pokemon were corrupted or had a corrupted (but stable?) item, so I traded over non corrupted versions of them from the repro cart, got their data, then injected them, then deleted the corrupted pokemon in Pokemon Chest. In the end the only things I lost were my battle video, my battle hall data and my hall of fame data, a small price to pay for everything else that works so much better now. At first I got a few "the save file corrupted, the previous file will be loaded" but it's been running smoothly now for a week with no crashes or issues. I can play voltorb flip, one of my favorite things to do as a kid, without the game crashing now! Thanks again to everyone who helped out, I really thought this may be impossible but so many people came together to help me find a solution. The internet is great.