Well, a bit of progress. I tried several options regarding the intake side of things. I used velocity stacks alone and velocity stacks with pods. The stacks took the pods about 1.5" away from the carb body. I was not able to get rid of the stumble, but there was an overall improvement in transition between throttle positions. So, I decided to try and get the needle to the middle position (one notch leaner than current settings). I went up to 135 mains (Tried these without dropping the needles and still got the stumble) and dropped the needles. I carefully inspected the needles and they look as new with no wear. Off throttle is much better now and the bike is much quicker at lower revs up to just over 1/2 throttle opening. However, I am now lean at about 3/4 throttle. I'll be throwing in some 140 mains this evening to see what happens. I had thought I was good with the 130 mains, but there was power left. The 135 mains pulled even better, so hopefully there is room to go to the 140s. These ported heads seem to like a lot of fuel, but man does it have some balls above 6500RPM.
Looking at the rubber piece used to attach the pods there is a v shaped lip facing outward, into the inner cavity of the pod (peak facing out, splitting the air), and ribs on the inside of the tube itself. I guess they are there to provide grip to the carbs. I am sure this is not good for air flow. So, I happened to have the old bread box filter setup sitting around, and low and behold, they have great velocity stacks that are offset to match the intake ports on the carbs. After measuring the diameter of the flute, I realized that this was the same diameter as the inside of the pod filter. I was able to combine the two to get what I would think is the best of both worlds. As stated above, overall transition through throttle openings is much better and idling seems to have improved (smoother) a bit. It still, and has always been able to idle at 900RPM, no problem.
I'll report back with further results. I hate dead end threads!!