One thing we did find out, quite by accident... I started getting low on gas as I came back into the pit (running out of gas seems to be a recurrent issue for us, but that's another topic)... the bike would start to run great as the gas was running out. So I take that as a clear sign we're just running rich, but it bothers me that we know we have the bowl height set correctly and we have the correct, stock, jets. So I'm kind of at a loss as to what the cause is.
Do open headers and velocity stacks cause these carbs to run rich?
Yes, absolutely. On the Fours it drowns them.
... intuitively I would think it would cause a lean condition, but thinking about it some more I guess higher velocity air through the carbs would generate a larger pressure drop, and therefor push more gas through the jets. EDIT: Thinking about this some more, since the float chambers are vented to the outside of the carb bodies less air restriction would generally cause a leaner condition... so I'm back to my original intuitive assumption 
As the velocity of the air in the throats increases, it drops in pressure. The pressure in the bowls then pushes the fuel up the jets. The tiny "step" area at the back of the venturi has one or more little holes nearest the outer edges where the air is moving more slowly than through the center portion of that Zone: this is "mid pressure" air, i.e., partway between the low-pressure venturi air and the outside (bowl pressure) air. This air is routed to the emulsifiers. Thus, the high pressure bowl pushes (heavy) fuel up the jets into the emulsifiers, where slightly-lower pressure aerates the fuel and improves the push up toward the low-pressure venturi.
So...if the bowl's vent air feeds are in a turbulent area, the bowls slow down their feed and the carbs go lean.
If the air hitting the back end of the venturi is moving too fast, this disturbs those tiny port feeds to the emulsifiers and lowers their pressures, so the fuel has a harder time feeding up to the venturi, as both are moving a lot.
If the air in the venturi (in the area over the jets) is moving fastest, it is lowest pressure and helps pull the fuel that got pushed up the jets into the engine.
So you can see, there's several places that can mis-calibrate your jetting....
Typically, pods and poorly designed velocity stacks (especially those that are the same ID as the mouth of the carb) cause turbulent air at the little emulsifier ports at the bell area of the venturi, so it is at too low a pressure to help lift the fuel from the emulsifiers to the venturi. Well-designed velocity stacks "aim" the airflow a little higher up, toward the center of the throat (like, right at the slide) to avoid this problem. If you don't have that option, diffusing the airflow (like using a screen across the open velocity stack) can help. But, this is a touchy adjustment, and hard to guess without a dyno or lots of track time. The Keihin engineer's best-guess for these was long rubber hoses from the air filters, which are under side covers to quiet the air, and ported across to each other on most Twins to further stabilize the overall pressure, so the air was pretty much like that in your living room by the time it hit the bell area at the back of the carb(s). That's how the carbs were intended to work, and the main reason the ram-air guys (roadracers of these bikes when I did it in the 1960s-70s days) seldom ran good top speeds. Those who instead enclosed their engines and carbs with fairings fared better, especially when using the long, thin-looking velocity stacks. This caused endless arguments about 'streamlining vs. open bikes', but the actual performance issue on these small bikes was the carbs, and how well they could be coaxed to mix. They are mighty simple devices, so you gotta live with their foibles a little bit?
The "racing" carbs, like the ones also found on the CL72 engines, had the 3rd jet to help in the last 1/4 of the slide opening for full speed, and they were GREAT. Keihin called these "power jets". They began to function at the upper part of the wasp-waist opening in the throat area, where the lower mainjet is starting to lose laminar flow, so the gas is getting "clumpy" and not well fed. The Power Jet then starts its action, increasing its feed to about 7/8 throttle, for lots more top-end power. That's why the lowly 250 Twin could do 90 MPH on a nice day, often outrunning its 305cc Big Brother.
