So two carb questions...

See pic: vacuum pipes on top of carbs: left has a cap, but right didn't have one when I got the bike. Is this a problem?

https://imgur.com/gallery/5rNhejg

AND

How much of gap should there be at idle under the butterfly valves? I just realized they shouldn't be closed, but I think mine were, or close to it. Is there a standard? I have a gap measuring tool, if you wanna get super technical.

My butterfly valves were also almost completely closed because the carb slow system does not use that much of it. Those vacuum ports are for carb sync only and they should be closed, it creates a small vacuum leak but I dont think it would be that sewere but by all means close it! Also change your vacuum hose from the carbs to the petcock in case of very small defect in the hose.

depending on year, maybe, there is a vacuum port on both left and right carbs but the right one is blocked off internally. So that's your petcock problem right there, plus by leaving the left one open it causes a massive vacuum leak.

The missing top cap all causes a massive vacuum leak. If they o ring is missing under the sync port on the carb top then it's a massive vacuum leak. You have to root out all vacuum leaks before you can tune.

Idling at 6k when starting cold on choke is normal. This is fast warm up mode. Read my blog post about fixing his, covers all of it.

so cap off that little vacuum nipple. Got it.

I bench sync'ed the butterflies. In order to show a measurable opening, they had to be moved to where the bike idled at 8000rpm first. 

I think I got the o-rings you mean. That was part of the rebuild. I will say that I have size 40 pilot jets with the bleed holes. I know they need to be replaced with the solid body kind, or it will probably be a little rich.

Another vacuum leak question: if the gasket for the exhaust pipes isn't stock/seem perfect, is that another spot for an exhaust leak?