Long story short:

My bike was sitting for a long time (5 months).
Before that, it ran perfectly fine.

I have drained the old gas,
changed oil,
and cleaned the carbs (not my first time, and due to my OCD I believe I cleaned them very well).

Now the bike runs perfect once it warms up a bit. However it is hard to start. When I try to start it after sitting for a bit on the first crank it will sound like its about to catch but it won't. On subsequent tries it sounds like it has a hard time getting gas. It sounds like it is running when I crank it but if I stop it will die. In order to get it running on its own I have to crank it for about 6 or 7 seconds.

I had a very deteriorated pet ****. The vacuum part did not work at all and the manual shut off would still leak when off. I replaced it when doing the work I mentioned above. The new petcock works fine. Does not leak and the vacuum works.

The last thing to mention is that my bike has a Yoshimura slip-on, K&N air filter and STOCK JETS (I know, It has a flat spot but its ok). When I was cleaning the carbs I forgot to note the the settings for the mixture screw. I set it to 2 turns out but the bike seemed to be starving under throttle in mid rpms. I am at 3 1/4 turns out and it seems to be running best with these settings once warmed up.

I believe that the starting problem and the choke problem are related. Any one got suggestion what it could be or what I could try to pinpoint the issue?

 

Check your choke cable adjustment at the carbs. The cable can stretch and if you set the ferrule on the casing at the clamp, it won't operate the choke fully. I visually set the cable to have no slack in the cable when clamped down. about 1/2 of the ferrule is clamped.

The stock pilot screw setting is 2 3/4 turns out for Cal models and 2 1/4 for 49 state ones. You are making the overall mixture rich by running 3 1/4. You could put an additional thin spacer under the needles to richen up the mid and then reset the pilot back closer to normal.