I made a previous post. Rebuilt the carbs and cleaned them. Gas was leaking terribly and it hydro locked my engine. Got it running again after pulling the carbs etc, changed some hoses and vacuum lines. Got everything back together and noticed it was intermittently running on 1 cylinder. We think the front cylinder is getting too much gas, probably a Petcock problem since we already cleaned and messed with the carbs. Any other suggestions would be appreciated. Also I noticed on the choke area there is a little nipple for air or something. There's no hose attached or air cap. Is there supposed to be something attached here? Posting pics for reference.

 

I think you will find that that stub off the top of thermostat case is a blanked off casting; at least it is on my VTR.
It's interesting though; one of many design features on the bike that show Honda either wasn't sure, changed the design or what I think it is; all sorts of options for what the bike was going to be used for or become.

As for the flooding front cylinder....is your float needle stuck open on that front carb? Tap it with the soft end of a screwdriver while you have the bowl drain open and closed and see ig that helps/