Pitted gear teeth may run for a very long time without issues. However if there was once rust inside the transmission the chances are good the bearings rusted as well. If you're hearing 'noise' that isn't normal then the chances are that the bearings are pitted as well. I've rebuilt and ran many a manual transmission with pitted gears and never had any issues. Now you might experience some if you intend to put a miracle mile on this transmission - but I suspect this probably isn't the case. I'm running one right now that was so rusty when I got it that it was physically stuck. I broke it loose with an air hammer, flushed it out with diesel fuel, put clean oil in it and have been running it for a few months now with out any issues.
