There were quite a few issues in your post - I will try addressing them all.
1. There is a PR for handling the issue where the joint name dissappears in the Joint Dependency dialog when you click on the down arrow to reduce the Follow Factor value. I hope it will be fixed soon.
2. Your joint isn't missing from the list, but the name simply dissappeared (due to the above mentioned PR). If you hit Apply you can see it is still there with the defined Follow Factor, which is why you can no longer select it from the list (already selected joints are filtered out of the list to avoid selecting the same joint twice as leading).
3. Finding the correct factor: PS allows finding the correct factor using the "Crank wizard". Otherwise you will need to solve the kinematic equations and enter a factor (or more likely an equation) manually. I think the Crank wizard is getting some enhancements soon in case it doesn't cover you use case.
4. I can't seem to reproduce your issue with the specific joints. If you send me the component itself I'll be glad to take a look at j8\10\12.
Hope this helps,