I'm very happy with my ninja-upgraded Ref3s. The Sean actually flew to my house, installed the upgrades, and then we drove together to the Lincoln City audio GTG last fall and let people have a listen.
Most interesting to me was when we moved the Ref3s out of the room were most of the "regular" speakers were and into the HT room, which had been converted to a Salk listening room. I thought the Ninja-modified Ref3s aquitted themselves well against most of Jim's work, at least in that room. Other than his top-tier speakers (which were near-final prototypes and absolutely fabulous sounding) I had a hard time distinguishing the Ref3s from the various Veracity speakers he had set up.
Now, take this with a grain of salt, as I heard the various speakers over the course of the day, not back to back, and, as we all know, a GTG listening session is much different than a detailed comparison in your home environment. But again, I found the Ninja Ref3s had that same, room-filling, pleasing sound that the HT2s (I think they were) had.
Sean is a great guy, BTW (as is Jim!).