Could dirt or "stuff" getting into the hole where the tranny meets the engine cause shifting probs on a 5spd?

 

I don't understand what you mean by this "hole where tranny meets engine". Do you have some cover(s) missing? Usually OEM is pretty well sealed to keep out dirt. Also, what are the shifting problems?

 

I don't know much about trannys. But where they bolt up you can see some of the tranny "inards". Also on the drivers side a bit back from there is another spot to see some "inards". It was acting like clutch or throwout was going, couldn't shift into gears, lurching at a light, etc. But after a rather audible thump to pull it out of gear it seems to work fine. Fluids are full, new clutch and slave 100,000 miles ago. Truck has nearly 200k. I wondered if some grit, road salt or something got in there and the thump was the stuff clearing out?