fwiw i had the same problem when i created custom followers, which were subsequently found incompatible with UFO, and in the end i decided to scrap the followers completely because the hassle of trying to get the system to work with both vanilla and UFO was not worth the hassle IMO. i instead opted to create an entirely new comapanion system from scratch that has nothing to do with the follower alias.
That's exactly what I'm aiming for in my upcoming unique follower mod. I love UFO just as much as I did love Toasters follower mods in Oblivion and Fallout series, but what really catapulted the follower experience in this games to a new level, was http://oblivion.nexusmods.com/mods/28977.
