2" is a lot, so obviously your saddle was much too low previously, so going back to that is not a good idea, and you saw positive results, too, so I'd scratch that. Back pain-- any pain-- is a real problem, though, so you need to do something.

I think looking at bar height is a good place to start; if the stem cannot go higher, have you considered replacing it with one that has more rise? I'd probably suggest starting there, trying to replicate the bar/saddle relationship you had before, so that you can either identify the angle of the back as the culprit or not.

It really could be any number of things, and working off just a text description leaves a lot to speculation. I mean, I presume the fitter is competent, so it's likely not any of the gross adjustment stuff. You really should go back to the fitter and get their input on this.

If, for whatever reason, you want to chase this down here, some profile pics of you on the bike at the bottom of the stroke, or even better, a video of you pedaling the bike on a stationary trainer, also taken from the side, would be the most efficient way to tackle the issue.