Until you restore your game folder to a clean 'vanilla' state you face the problem of conflict and possible CTDs. You must remove them all, whether installed via Steam, NMM or manually and re-install them with MO.
It is quite simple, ALL mods must be managed by MO to avoid the 'unmanaged' indicator appearing next to them. Really!? You spent days searching and haven't found the answer despite posting in a topic that answers the question! I greatly appreciate any time that you can spare to help me out. The mods I'm trying to eliminate have to do with lock-picking, gauldur's amulet and more descriptive mine map markers. I'm also thinking about installing USLEEP ( Is this a good thing? ) and want to ensure that I have a good clean set of mods installed prior to doing that. I've been having occasional CTDs and want to first eliminate these unmanaged mods as a possibility. Would someone be kind enough to point me in the right direction so I can read up on it myself ( preferably ) or tell me how to do it if there is no explanation posted?
I've found mods that do the same thing plus additional things and I want to use them instead of the unmanaged mods. I try to find the answers to my questions on my own so I can learn better, but this one has me stumped. I've spent several days looking around trying to find an answer to the question of how to remove unmanaged mods from my MO installed mods list.