Running it off one cylinder is fine (and if you try to keep both you must keep the vacuum circuits separate as bleed from one cyl to the other will screw up the running at idle). You just need a small restrictor in the vacuum line. These aren't hard to find as they are needed when you balance the throttle bodies via a vacuum gauge. There are probably already vacuum ports on the TBs for syncing the TBs so might as well use that.
I've never used a vacuum gauge on a moto other than to sync carbs/tbs. It'd be pointless for me, but I don't ride around trying to get great mpgs - I'm more the flog it and have as much fun as I can type
