I got the next size up main jet too. Should I hold off on that one until I get the low speed sorted? My plan is to install the new pilot jet, turn the mixture screw back to about 1 3/4 turns and start from there.
First things first; address the low speed circuit first. While the motor is cold, Install the 45 pilot (slow) jet. While you have the bowl off, take the A/F screw all the way out and check the washer, spring and o-ring for correct assembly. I would suggest a new o-ring, over time, they flatten out and I have seen them turn sideways in the bore. Blow out the A/F port to make sure it is clear and reinstall the A/F screw assembly; set at 2.5 turns out.
Start the bike using the enrichener for about 30-60 seconds, then push the enrichener all the way in and use the throttle, if necessary to idle the bike for a few minutes. Take a couple of spins around the block to get the bike up to operating temperature; makes carb tuning a bit more of a challenge; easy to burn knuckles but, operating temp is necessary. Quick warm up and a couple of spins around the block will do it. Once up to operating temps, set the idle rpms between 900-1000.
Turn the A/F adjuster all the way in. The motor should stumble and possibly die when the adjuster is all the way in. However, if there is no change, pilot (slow) jet is too big. Now slowly back the A/F adjuster back out listening to the exhaust and watching the motor vibration. The A/F screw should end up between 2-3 turns out to produce an even exhaust note and minimize the motor vibration. You may need to turn the screw in and back out several time trying to find the sweet spot. Believe me when I tell you that even 1/8 of a turn will make a difference.
Once you have this right, the motor should respond without hesitation to a quick blip of the throttle, smooth idle, no backfire, no cough, just a quick throttle response. Once you have this sorted out, you can move on to tuning the mid range (needle) and WOT (main). Once you get the slow speed issues sorted out, fill the tank, take a 100 mile ride trying to maintain between 65-70mph. Fill the tank and check mileage; pull the plugs and take a look. You can use the mileage to adjust the needle; if mileage sucks, drop the needle; if mileage is too good to be true, raise the needle.
Once you are happy with the needle setting. You can get a handful of new plugs and tune WOT with plug cuts.
Keep us posted on results.
You can also check out the Nightrider section on the CV carb.
http://www.nightrider.com/biketech/hd_cv_mods.htm