If I remember correctly there is a flat part on the rotor shaft. The setscrew should meet up with the flat part. If it is not then you will need to remove the distrib and fix it. Again the picture in the above article should help you align it.
After reinstalling the distrib and getting everything straight I would suggest getting a timing light. There is a nice article on how to use it here
zerothread/358264. Either that or you can play with the distrib a bit to get it to fire right.
*after* you get the ignition timing down, I would also check the usual (plugs, cables, fuel injectors) as to why it's running rough. But right now I would say ignition timing is way off.