To OP: Your alignment looks very good, just FYI: the ranges you have are not for 5th gen 4Runner, but your measurements are in spec. And considering everything you have done there should be no issues you are experiencing…
For the reference I have 2013 Trail (with KDSS), with lift and same tires as yours… truck has 67 k on the odometer and tires have about 40K –and that truck is smooth as butter…
Here is what I would try first: change your “toe” so the tires are pointing “in” very so slightly and since you mentioned your truck pulls to the right I would make right front wheel “toe in” to the left… you can do it yourself by adjusting right Tie Rod- I would do half of the turn and see if that will make a difference, it is very simple to do (10 Minutes job at a most) and you can always turn it back at any time.
Another possibility is wheel (s)… When I had my 4th gen (I was a second on owner) I have also had to chase vibration issue, the culprit was “bent” rim… you could not see it and tires would balanced, however the issue was resolved only after I have replaced that rim… I know on the new truck chance of the bad rim is small, but you never know.
Hope that helps.