A few things stand out at me. I'm by no means an expert nor am I very experienced, but that temp swing is really big. That worries me. Usually a temp swing of 2 degrees is something to worry about. What are you using for a thermostat? Proportionals are really the only thing that should be used for incubating because they help dampen temp swings. Also, if you don't have any water bottles in the incubator I would get some in there. They help stabilize the temps and hold temps when you open the incubator. As for your substrateless, people generally still put some vermiculite in there or something of the sort to ensure the water doesn't evaporate, which is much easier to do with just water in a tub.

Other than that, those green eggs are definitely bad. I would wait on the third egg starting to turn green. If the third one is touching another egg don't worry about it if you can't get it off the good egg. I had a bater full of bad eggs last year and didn't take any of them out/apart from the good eggs. One egg that was turning green made it all the way to day 52 when it finally died. Three eggs made it to the end (all attached to eggs that started rotting at day 18). The babies all ended up train wrecks, which would explain why they were randomly dying. Perhaps that's why yours are dying? I wouldn't be too surprised if that happened from the temp swings. This year I'm totally revamping my incubator in case something was wrong with it. I had a helix running and I don't think I ever had more than a 1 degree temp swing, but who knows. Good luck with your eggs, I know how you're feeling.