I got a set of vacuum gauges for my bike last year, and after setting the little damper thingies, put it on my Shadow. I had used a "bench sync" procedure, where it says to set the butterflies so only the top hole is visible. Well, that was close, and it ran OK, but I decided to check it with gauges.
End result: there's nothing like reading it with gauges. The balancing screw needed quite a bit of adjustment. When both needles were getting close to the same reading, the RPMs went up and up, necessitating the throttle stop screw turned WAY down...like maybe 3-4 complete turns. Blipping the throttle, the engine revved much quicker, and a test ride confirmed it. Nice burble on deceleration, ran nice and smooth, mileage was about the same, all wins in my book.
As far as your issue, pods and the DOHC carbs are a pain, as the carbs like to see a certain amount of vacuum. The stock air box provides this. Rejetting the carbs to compensate for the more open exhaust and more open air will be necessary, but I think the previous owner went a little overboard.
Check the plugs: If it's running rich, the plugs will be darker, almost a sooty dry black. If they are light to medium tan, then the mixture is probably about right.
I hope this helps. Keep us informed, and we'll help if we can.
Luke M
Used to have a 1979 CB750L, sold it as a parts bike, now riding a slightly modified 1984 VT700C. Network/Field Engineer. Central OH, USA, Earth, Sol System, Milky Way Galaxy, Universe.