The S&S carb is a good carburetor, easy to adjust, easy to diagnose problems, very user friendly... but certainly not the best for the street. One a drag bike, yes. But street would be a Mikuni and next to that, EFI.
As far as the Flush pump (you mean Accelerator Pump) goes, it should not be overlooked. With the amount of Ethanol in the fuel now a days, it's a very common problem for the accelerator pump nozzle to plug up and not fan out like it should, along the with rubber pump diaphragm not functioning correctly as well. The base setting for the accelerator pump screw is 2 1/2 turns out from bottom.
With the mixture screw. Base setting is 1 1/2 turns out from bottom. If you are at 2 turns or more out, you have another problem with carburetor. Finale adjustment will usually end up around 1 1/2-1 3/4 turns out. If more than that, you likely have an intake leak. If you have it adjusted in less than 1 1/2 and bike is still running smooth, most likely the fuel screw is worn out (see pictures above by Franco)
With motor at operating temp and at idle, the correct way to adjust the fuel screw is to close off the accelerator pump screw all the way. Doing this the idle will drop, but motor should not stall. If needed, you can adjust the idle up just a little so it does not stall while making adjustments (keep idle around 1000 rpm) With accelerator pump screw closed off, you now adjust the fuel screw from your base setting of 1 1/2 turns. Adjust slowly in watching the amount you turn needle, till the motor RPM start to slow down. Now turn back out, watching the amount of turn till the RPM start to slow down. Go half way between these two points and leave there for now.
Now go back up and turn the accelerator screw back out 2 1/2 turns and adjust your idle back to around 1000 rpm.
At this point you will have to take the bike out and test ride to see how it responds to throttle under load. If it hesitates, you will need to adjust the accelerator pump screw either clockwise or counterclockwise. But, you will only be adjusting this 1/8 turn at a time. Adjust and test ride and if it gets better, then keep going that direction until it's 100%, if it gets worse, adjust the other direction until it's 100%
If you are getting a lot of deceleration popping, and you know exhaust gaskets are new and not leaking and everything else is good, turn the fuel screw out a little at a time ( 1/16 ) until the popping is better. 1/4 to a 1/2 turn is too much. These needles are fine adjustments. And keep in mind, some exhaust systems, no matter what carburetor or even fuel injection, they will still have some deceleration popping.