Ok I wont beat around the bush. I got a virus, a bad one. I am just regaining control of my pc after two months of fixing and repair of windows. When I first tried to play skyrim all my mods were gone. I checked the Nexus mod manager and found that it did not work any more (due to some windows issues I still have). I figured that was the issue. But on a hunch I went into the skyrim menu and checked the modes there. I found that they had somehow all been disabled so I enabled them all and they all came back and run fine as best as I can tell. However there were many personal modes I had made to some of the mods I downloaded. Those modes are now no longer working within the mods I downloaded. It has been a while since I used the creation Kit and don't remember much. So Before I begin all over again. I thought someone out there might have some suggestions for me on how to get them to work again. Remember the original mods are working fine its the modifications I made to them that seem to have stopped working.

Thanks in advance.