I'm not sure if I missed it somewhere, but is there a way to preserve priority organization across profiles? I have a profile mostly set up the way I like it, but I want to move from AFT to EFF and I really don't want to have to shuffle all the other mods around again.
If I've interpreted your question correctly, you have an existing AFT profile , you want to create a new EFF profile. Also the priorities in EFF profile should be the same as the AFT profile when you start using it. In the MO wiki tab Profiles this is discussed in section 'creating profiles'. Use 'copy' to duplicate your AFT profile and name it EFF. Though I have to admit priorities aren't mentioned.