I've got similar issues at present and the mech hangers been checked.
Assuming B tension, hi / lo set screws, mech hanger and chain length are all ok some thoughts:
Have you
got the cable routed on to the correct side of the pinch bolt on the mech?
tightened or slackened the loop of cable entering the mech or introduced tight bends elsewhere?
taken the cable out of the mech, held the cable between your fingers and checked how easily the inner indexes back and forth?
tried turning the cranks and moving the mech by hand?
If everything incl mech hanger and mech is ok and the cable is sliding freely it's possible it could be a malfunction with the indexing in the shifter itself. Not seeing any correlation between the new jockey wheels and the problem. If all else fails borrow another shifter and or mech that does work and see if you can get it to work on your set up – process of elimination…