G'Day,
There's three things I'd recommend in addition to the other advice here.
1. Get a foot file and manage the size and surface of the callouses. It will polish them smooth.
2. When you release the ball, point your thumbnail to the back of the hole. Remember to "release" the ball, not extract your thumb from the hole.
3. Tape. I cannot emphasise how important tape is to a good fit. No matter how good your driller is, your ball only fits on the day it's drilled. Every other day, the thumbhole probably needs adjustment through tape. White tape is for gripping and goes on the front side of the thumbhole, centred down the gripping surface of your thumb. Black tape goes in the back of the thumbhole and is for spacing the hole size to fit. Alternately, you can use a cloth tape that adheres to your thumb. This comes in various grades of slip. Tape is essential to a continuing good fit.
If I don't have thumb trouble (and it's very rare), then nobody should have to. You don't need to put up with that sort of discomfort. Good on you for investigating your problem. There are some good solutions in this thread.
Good luck with it.
Jason