I agree, let us know how you are doing. Is it better? I worry about the exact same thing as Anniebrooke. Fingers touch all sorts of things and then could introduce that bacteria to your urethra. Let us know if it is better.
The person doing the fingering has to have scrupulously clean hands and nails. Hurting when you pee could come from an infection or from something physical your partner is doing. If your partner is not doing anything to the urethra I would suspect bacteria rather than scratches, and hands are often laden with bacteria.