After re-checking timing, valve adjustment, carb sync, bringing air filter and all jets to stock
I still have a bit of hesitation from idle after the bike warms up. I am also getting some popping from the exhaust on deceleration. There is a slight exhaust leak - I can feel some air coming from between the mufflers and the headers. I assume this is causing the popping on decel.
Quite possibly.
When I took the mufflers off I found there is no gasket or any material in the collar where the muffler slips over the headers. I did not thoroughly check for leaking where the headers meet the cylinder head but I plan on replacing those gaskets when I seal up the leaks by the collar.
The crush gaskets used there, are usually copper colored, but blackened during use. Point of a screwdriver should scribe the carbon to show copper. The gasket must be dug out of the pocket for renewal.
Was planning to just use Permatex ultra copper to create a seal. Is there a cleaner/better solution?
Permatex would be a hack, best employed after the apocalypse. Buy some new crush gaskets. ...and don't let the muffler system be supported only by the header flange bolts during assembly or they will crush unevenly and leak just as bad as before renewing if not worse.
Would the exhaust leak be causing the bike to run rich at idle thus causing the hesitation?
No.
Go back and reset the pilot screws. These screws are adjusted to obtain smooth acceleration when the throttle is opened.
If the factory setting of 1 1/2 turns out from seated doesn't cure the hesitation. The begin with them at 2 turns out and perform the following test.
Mark your throttle so you can determine the halfway twist point.
Operate the bike, select top gear, and ride a short distance so that the engine is at idle RPM. Snap the throttle to the half way point. The engine should smoothly pick up speed without stumble or wheeze. There won't be a lot of power or torque down that low in top gear. But it should try to do what was commanded without complaint. If it does stumble, then turn all the screws inward (022a carbs) about 1/8 turn and repeat the test recursively until you can get the desired response.
If you turn the pilot screws in too far, you can grab more throttle than 1/2 twist. But, then you run the risk of carbon fouling the plugs during periods of idle, and creating stumble from misfires during acceleration as the plugs clean themselves.