JSGME will reverse any odd effects you have by taking out the new file and reverting to your old ones. I don't use the exact mods that you do, but I tend to ignore the messages and check out what has changed and whether I like the change. If something freaky happens, I go back to JSGME and take the mod out.
I recommend you try one mod at a time. Once I made the mistake of installing over a dozen mods at one time and spent a couple of days trying to work out which one was causing CTDs .
I put my least favourite mods in first with my preferred ones last. This means that I get the full benefit of my preferred ones and accept that I may lose something from the earlier ones.