Took the reel apart cleaned it up and reassembled it. Noticed that it is really rough now. Took it apart again and kept messing with it and determined that the main gear is rubbing on the crosswind block when it moves up behind the main gear. What am I missing here?
It's a pretty odd problem to occur, I'd check for a few things:
1) Make sure the Oscillation gear is seated properly, as well as the crosswind block/spool shaft slider
2) You might be missing or have too much shim washers on the main gear shaft, usually on the left side of the reel as you're looking from the reel stem/foot. I don't remember if I've seen any shim washers on the right side for Penn, which is also the usual case for other brands. Though I've seen some reel which do have shims on the right side.
Check the that goes thru the slider, sometimes if it doesn't seat right it will scrub.