Welcome to the gastroenterology community! A 100% gluten free diet is very difficult but I would recommend posting on the celiac disease community and see if they can give you any advice you stay gluten free. The biopsy for celiac disease is more accurate than the blood tests. EOE can be very difficult to treat, what are all the treatments you have tried for this?
If you have celiac, make sure you check to see if you cross-react to casein, the major protein in dairy. Many celiacs do.
Two months on a GF diet is basically just a start. It's going to take a fairly long time to make enough changes to the cells of your body, and your body as a whole, to really feel much, much better. My husband 'hit' gluten issues at 50, and it took over a year to start to really feel a LOT better. He saw changes along the way, but it was a full year until we knew 'something' was still 'off' and started investigating other things and found the cross-reaction to casein.
The MC is probably tied in with the gluten issues, so hopefully that will also do better as your gluten issues get tamped down.
The EOE is more problematic. It may require going of a much more strict diet. Try to find a doc who specifically deals in issues such as celiac and EOE. Your doc sounds a bit behind the times if he rechecked the results of the biopsy with a blood test. The blood tests are notorious inaccurate. Fecal antibody tests and gene tests for celiac disease would have been a more informed option.