Welp, my dealer finally (3 months) got in the EFI pipe so I installed it last week. Guess what, all my rough running problems are pretty much gone. I was getting stalling idles, mid corner hiccups, rough running.. It seems to have all gone away. I can hit the starter button now and she will keep purring till I take off, which I could never do before. Also my idle seems to have dropped a bit...pop....pop....pop.
I surmise that the computer cant handle (basically) wide open exhausts, so I guess contrary to what others have stated about the flexibility of the oem EFI computer, I think its fairly tight in its tolerances and allowable changes. The bike ran, but pretty poorly and it felt very unrefined.
The bad part... I did notice a fairly large reduction in power with the EFI silencer, so I guess its a tradeoff there. I'm in the search for a pipe somewhere in between the EFI and the megaphone - I need more character and sound than the EFI, but more back-pressure than the megaphone. Maybe there is some way to mod the megaphone.. making the exit diameter smaller perhaps?!