I don’t think teshuva and tefilla will affect your negative thoughts- unless you daven for Hashem to help you in this area, obviously. I’m not really sure how to work in this issue. Here are two suggestions:
1. Work on your bitachon. If you believe that every mistake you make is from Hashem, you won’t beat urself up about it.
2. Every time you catch yourself thinking negative thoughts about yourself, replace them with positive thoughts. I remember reading a list of positive things to think on divreichizuk.com. If you can’t find it there, just google for a list of positive thoughts.
I remember hearing Mordechai Weinberger LCSW talking about mind chatter. He said that if someone else would tell us the things we say to ourselves sometimes, they would be labeled bullies. Don’t bully yourself!
Hope this helped!