Apologies, I didn't mean to make it sound like it was a ninja only thing. It's just that I had noticed a complaint about Ninjutsu being problematic, which may have been from a player who only plays ninja. From what I recall when ninja was first introduced a lot of people discovered that they had lag issues that didn't exist for any of their other jobs because ninja is so tightly tuned.
As you say, it's affecting all your jobs which suggests it's more than lag (you've checked that). I had a problem between 3.25 & 3.35 which introduced a bizarre issue that seemed to only affect me. When I logged on for the first time in a day I would get a 90k disconnect after playing for 5-10 minutes. When trying to log back in it would tell me my character was still in the world. After I waited 5 minutes & got back in I wouldn't experience the 90k again, even if logged in for 12hrs+. Next day the same scenario of 90k, log in then stable.
Why I mention this is because there's definitely potential for inter/intra server discord that we have no control over. I believe that you're experiencing this. I hope a hotfix or server maintenance will sort you out.