When you are checking the vacuum and syncing the carbs, you need to restrict the flow from both carbs via little flow valves. They should have been included in the kit.
Vacuum should not be left open, or it will cause issues (such as the bike dying). Left vacuum goes to the petcock, as I am sure you found out, and the right goes to the emissions system. There is a procedure called coastering/marbling that gets rid of it (the right gets plugged)
Now, the noise you hear, is it a tapping sound, upper cyl? If so, probably the Automatic Cam Chain Tensioners. They begin to get weak, and can cause the cam chain to jump, affecting timing. If they're failing, switch to manual tensioners instead of replacing them.
Your issue may just be due to dirty carbs, with the other noises of the bike possibly leading you down other paths. Run a heavy dose of seafoam in your gas for a few tanks and see where you land?
Both of my bikes start without choke fairly fine, as long as its warmish out. If it's colder, it's just easier to hit the choke.
Welcome, and best of luck!
PDF Manual: http://www.tocmanufacturing.com/File...nd%20Parts.pdf