Bandit 600S Air/Gas Mix Question
 

Hi, Im relatively new to riding street motorcycles, I have some experience with small dirt bikes but nothing major.
I have a question about my air-gas mix.
Bike is a 1996 Suzuki Bandit GSF600S
The bike was runnig great the first 2 weeks I had it then it out of nowhere was runnig very rough and I hardly made it to work that day, later it broke down on me. I noticed the previous owner has the wrong size air filter in it leaving slots on the sides for dirt to go straight into the carb. Asshole.
Here is what I recently did to improve the bike:

-removed carb and both sets of shoes. Pulled all the jets and replaced them with new ones
-Cleaned carb housing parts and did a full carb rebuild with all new OEM parts
-Replaced all 8 shoes for the air box to carb and the intake to carb and crushed them all prior to installation.
-Removed all 4 pilot screws as well and replaced including the little O-rings.
-Set Pilot screws to 1 5/8 turn out, reinstalled carb and ran the bike for about 10 min then again removed carb to did a secondary pilot opening of another half turn leaving all 4 roughly 2 and quarter turns out.

After reinstalling everything I noticed it still runs rough. It cranks up just fine even with no choke on it which is nice but its acting like ts getting too much air but I dont see how thats possible with the pilots only a hair over 2 turns out, but like I said before Im new to this whole thing.

My question is does anything in the procedure I did sound wrong? and I forgetting something? could running the bike for 2 weeks and even longer by previous owner with wrong filter and dust running through the card damage the motor?? from riding dirt bikes dirt gets in the carb sometimes and doesnt hurt the motor.
Please help me get bike running well again, Thank you