You didn't say anything about the face of the guitar. If it is starting to pull up, nothing you do to the neck is going to work.
This is where a Bridge Doctor system really shines.We've had a couple of discussions about the system, which can be found by entering Bridge Doctor into the filter for a Forum search.They really work.
If you have intonation problems after all is said and done, a compensated saddle or nut will cure those.
A good luthier should be familiar with all the tricks.
I was having intonation problems with my 12-string, which is built like a brick shit-house,but Michael Lewis of Grass Valley, Calif.carved a beautiful compensated saddle for it.