Are you addressing the soft tissue of your foot?
Sounds like this is not a new situation so it can take time to see the pain resolve.
Clearing up the nerve irritation is key.
Yes, you feet may be uncomfortable because they are in new positioning when wearing correct toes. Changing any habit or position can be tough. Muscles, fascia which haven’t been working in the past are now called upon with the new positioning. Dose response when wearing them.
Do you wear tight fitting shoes?

Do you do any foot strengthening exercises?
Correct toes may start to show your feet correct positioning if you are not wearing tight fitting shoes which squish your foot.