Did you do the check for air leaks? Does the throttle cable have some free-play and return to stop when released? Does the throttle shaft return to the idle stop screw?
The pilot jets may be a bit small, but IMO, you can't tune the carb until you fix exhaust leak, install the pipes, verify ign. timing and get a ball-park synch. on carbs. All is suspect ATM.
I realize you started in a hole with a bike previously fouled-up, but "one step at a time" is required - no skipping ahead will advance the cause