So long as you can do Tuneboy tuning with the new dyno then yippee. I expect to see some new supercharger tunes soon.
Did you ever figure out that going rich thing when quickly jumping the throttle? You mentioned accelerator pump thing. I'm too lazy too look for that thread now but I was going to suggest you look at changing the L maps in TuneEdit. These are the low throttle (<6% throttle) fuel maps and I don't think they are being changed much when dynotuning. You may need to ramp up the tables more to align with the main fuel tables so transition is smoother.