When I reel my pro qualifier the bottom of the pinion gear rubs against the the frame and creates a rough feeling. It's like it doesn't sit right when the spool shaft is inserted. Do I have a bad gear or spool? Please help!

Bring it to BPS

It has a little piece that comes out to grease the gear right? Did you out three obv screw in there? It is to long and the hear is hitting it.

I had the same issue with my new PQ.  The pinion gear just didn't fit well and "floated", which caused it to grind when reeling and sometimes didn't connect with the main drive gear.  I took it back to BPS and exchanged it, but the pinion gear on the exchanged reel seems to do be just as questionable.  I'll be very careful when cleaning the pinion gear!

You're misinterpreting something. There's nowhere for the pinion to "float" to nor is it long enough to hit the frame. If anything, inserting the spool will serve to further support the pinion gear as the spool shaft is inserted. The more likely scenario is the spool is making noise as it turns. Is free spool good? Try loosening the tension cap, removing and reinstalling the spool, swab the brake drum with light oil, and readjust the spool tension to just where there is no lateral movement. If that doesn't do it, it should be exchanged or serviced. Let me know if I can help. 

Mine makes a weird clacking noise sometimes too. Brand new 7.1 :1. I think it could be where the brass part engages the cross pin on the spool.

Mine makes a weird clacking noise sometimes too. Brand new 7.1 :1. I think it could be where the brass part engages the cross pin on the spool.

This is only intermittent.

Your weird clicking is probably the pawl and lever wind gear. Mine does from time to time also.

Interesting thread.
I just started having some issues with my Pro Qualifier.

Will take it to Wayne Knabe to have him fix it.

Last Pro Qualifier I will ever buy.

Shimano, here I come!