Thank you for the additional information.
We may have two problems going on here, but I want to attack the obvious problem first. The carbs have plugged up pilot jets. If a bike sits for more than 30 days with gas in the carbs, it evaporates and leaves a shellac type substance behind that plugs up the tiny orifice in the pilot jets. When you have to turn the choke on to get it to idle (somewhat) you are providing an alternate fuel source which essentially bypasses the pilot jets, allowing the bike to run.
You will have to take the float bowls off the carbs and carb removal is mandatory. You will have to take off the fuel tank to access the carbs. Use some caution if the float bowl screws are so tight that they want to strip. If that is the case, use an impact driver (preferably Snap On because they work so much better than any other brand, esp. the cheap chrome ones) and break all the screws loose. Once they are loose you can remove them with a screwdriver.
Remove the float bowls and all the jets. Here is a diagram that shows the break down:
Reference #18 is the jet you are primarily concerned with cleaning, but since we have them off and apart, we are going to hit them all. A good way to clean them is soak them in Pine Sol. Cut the pine sol 2 parts of Pine Sol to 1 part of water. You can put the jets in the float bowls and fill the float bowls with the cut pine sol. Keep an eye on them and soak them until the brass looks clean again. Rinse with water until all signs of pine sol are gone. Put the jets back in the carb bodies and sync the carbs. Sync is a critical step because even spotlessly cleaned carbs will not operate properly if they are out of sync.
After you get the carbs cleaned and synced, lets move on to re-addressing the stalling when put in gear. Make sure when you sync carbs that the idle is set at about 1000 RPMS. An idle that is too low could cause the symptoms of stalling when kicked into gear, although it is not the only possibility by a long shot.
Let me know how you get on with that and where we are at.