I've found that bike fit is as much art as science. Some people know the rules, set things up according to the angles and measurements they've been taught to use. Others are a step beyond that -- they've got a good eye for when a person's bike fits them and when it doesn't, and they have a feel for when they should bend the rules a bit to work with an individual's physical situation. And often there's a certain amount of trial and error involved.
The first time I had my saddle height changed by the best bike fitter I've worked with, I didn't realize yet that he was the best bike fitter I would work with. And I felt that he had dropped the saddle way too much -- my knees just felt wrong. But it turned out that he was absolutely right, and I did get used to it and was happier for it. One time I mentioned to him that I had elbow problems that weren't caused by cycling but were made worse by it. He measured my shoulders and told me that I was on the line between my current handlebars and ones that were slightly narrower. I kept the old handlebars and resolved the elbow problem (with a larger mouse for my work pc). But a few years later I was having just enough neck and shoulder pain to make me switch to the narrower bars. That did eliminate the pain, though it also changed the way the bike handled, which took a bit of getting used to.
I hope the changes being made help with the problems you've been having. Bear in mind that you might still need to tweak things after you've ridden the new setup for a while.
- Gray 2010 carbon WSD road bike, Rivet Independence saddle
- Red hardtail 26" aluminum mountain bike, Bontrager Evoke WSD saddle
- Royal blue 2018 aluminum gravel bike, Rivet Pearl saddle
Gone but not forgotten:
- Silver 2003 aluminum road bike
- Two awesome worn out Juliana saddles