The first thing I can suggest is you go back to basics and decide if you are experiencing wobble or weave.
Then look at what causes whatever your symptoms are.
There are three basic areas: bike; environment; rider. All are variables which need to be considered.
For example,
the same bike can perform badly for one rider and well for another rider simply because of the different weight of the riders!
Installing accessories e.g panniers and/or top-boxes can affect handling.
Different road surfaces can affect handling.
Unfortunately, it is a methodical process of elimination - as you have already found!
As you have been doing, you have to check the bike is set up right: wheels balanced; correct tyres & pressures; rear wheel adjusters set correctly; wheels aligned correctly etc so you can rule out the basic set-up. Then take a critical look at your accessories/mods to see if they could be having an effect. Finally, consider if you as the rider could be contributing to the problem - may need to eat more pies!
Good luck and let us know how you go on. Have you heard from others with the same probs?