You have gotten some good information from others. Some of the methods that I have tried are:
Originally Posted by Deckled Edge
1. The finest point red Sharpee pen, gently applied, will work on sizeable pinholes.
2. Use a fine needle embedded in a pencil eraser and gently (I mean gently) scratch the base side of the film. This will cause the enlarging light to diffuse when passing through the negative and work at retouching the pinholes.
3. I agree with Ed about the stop bath and stop bath strength. I dilute my stop to 1/4 normal strength when using pyro developers.
4. The Veronica Cass dyes are great. I use an Adams retouching machine to magnify the area to be retouched. That makes it easier.
5. Check your film holders (if applicable). Dust can be a culprit as much as stop bath strength.