hmmmm.......well, 86main, I can't imagine that the "smoke" that crept into the cabin of your car came from a manual transmission (your car is a manual is it not?). The transmission is a pretty tight box and your car was moving on down the road.
Are you sure it wasn't hot/burnt "clutch" you were smelling?
You might check that cam cover to make sure it's not leaking and dripping down on the exhaust pipe.
http://www.ft86club.com/forums/showthread.php?t=45097
How does your clutch adjustment feel ..... any different?
humfrz