Since you went to your fitter to have the knee/ankle pain alleviated and he did that, I am going to assume you went to a good fitter with a difficult personality but he/she knows what they are doing. My first thought upon reading your post was that you may need to adapt to the new position. It sounds like for the most part your position went back and up. As such, this will change your weight distribution on the bike. Your new more upright position transfers weight from your hands to your sit bones and you are now sitting differently on the saddle or possibly even on a new point on the saddle.

I have had several bike fits and have my position duplicated on all my bikes (10) so I know they all fit properly, however after not riding consistently for 15 months I returned to riding and my butt hurt! I typically ride 5k miles per year, centuries and my butt hurt! I did not change a thing. Took about 3 weeks of riding consistently or really just getting in the saddle for at least 30 minutes for me to feel like my old self again. So not unusual at all to have some soreness after a position change.

One caveat to my post is that I am talking sitbone pain, not pain or numbness in the soft tissue areas.

Finally you you may want to look at different saddles. Some saddles are designed for different positions. You also do not say the length of your typical ride but in general the longer the ride the firmer the saddle. A soft saddle with a lot of padding feels great at first, however as the longer you sit on it or more weight placed on it via your more upright posture, the padding collapses and begins to cutoff blood circulation leading to numbness/pain.

My guess is that you just need a bit of saddle time to get your body used to the pressure of more weight on the saddle vs hands.

Another thing I forgot to mention previously is saddle width. The more upright position often requires a bit of a wider saddle. You can go to a bike shop and have it measured or DIY by getting some paper or cardboard and getting your rear end damp and sitting on the paper. You will see a print of your sit bones, measure the distance center to center and that will give you a measurement to use to help you select a saddle width. Too narrow of a saddle will typically put too much pressure on the sit bones, too wide on soft tissue.