Took the 12-string in to Lee and he basically said I was on the right track with my adjustments, and advised me to cut the slots in the nuts slightly deeper to make the action on the first few frets better, and then I might have to carefully file down a few frets that are "noting out" farther up the neck.
After he looked at it I realized that my other two main guitars could use some neck adjustment as well, and I was surprised how much better the action got with just a little adjustment. Well, on the Martin D-15 it got a little too low on the high E string so I shimmed that end of the saddle and backed the tension on the truss rod about 1/4 turn. Niiiice. Just high enough not to buzz.
I need to find my razor files to do the 12 string properly.
And my backpacker needs it's saddle filed down a bit lower.