Well I decided to follow the advice and remove the secondary plates and T the two vacuum lines between cylinders. You know how sometimes you read about all these modifications and most of them result in a minor or no noticable change. This was not one those. 90% of the stumble and roughness at 3500rpm is gone. The bike not pulls smoothly, even when doing a 4th gear roll on from 1500rpm. You can cruise all day at 3500 without any surging. Based on the great advice I also ran extension lines from the vacuum ports to make balancing the trottle bodies a very easy task. The job took about 2 1/2 hours, with most of that spent drilling out (very carefully) a rounded screw in the secondary plate. Great advice, I might just keep this bike after all.