I know you spent a lot of time setting the position up, but in my experience you'll still need minor tweaks, and it takes a few longish rides to sort out finally. I've been doing a few mm here and there over 4 rides and think I'm just about there. Yesterday I rode round with a spare stem just in case I decided that 100 was better than 110mm. (It didn't get used).
Some pains just go away as your body gets used to what you are putting it through. As I got fitter last year most leg pains (knee, achilles) went away, & I ended it with shoulder pain, something I've never had before.