If you think it is the actuator opening the bypass valve between shifts, you could try a restrictor in the vacuum line. Mine was having the opposite issue because of the lack of vacuum with my big cam ... closing too quickly on accel. Mike at Whipple sent me the restrictor which fixed the issue. Initially the hole was too small, which created what was almost like turbo lag ... so I got a tiny drill bit set and opened up the hole slightly. Now it's perfect.
There's no reason why it wouldn't work in reverse ... slow the opening of the valve.
It is a 1" long step-tapered cylindrical brass that pushes into the vacuum pipe on the actuator, with a tiny hole in it. Looks a bit like a jet out of a holley carburetor that has been stretched. (minus the thread and screwdriver notch)