So, I've spent a few minutes looking into this. Guhl Motorsports does a bunch of tuning and flashing on sportbikes. A quick search revealed these posts on a VFR board:
"Please keep in mind that we are currently only able to reflash the 2006-2009 VFR800 ECUs. The older ECUs is a whole other project and I'm not even sure they can be reflashed.
I'm still looking for someone local to Ephrata, PA 17522 with an 2006-09 VFR800 to put on the dyno.
Looking at the fuel maps, I see an area in the 2500 RPM range where they are taking away a bunch of fuel and I believe that is a possible cause for the low throttle/low rpm smoothness issue. Since it is in the low load mapping, which is controlled by manifold vacuum and engine speed, it is nearly, if not, impossible to fix with a power commander that uses throttle position and engine speed to control the fuel change. It's like trying to hit a moving target. It is something that is fairly easy to fix in the ECU.
Thanks,
Don Guhl"
On the older ECUs from Don Guhl:
"ecuunleashed or pisani engineering must cut open the ECU to reflash it. We do not. We have reverse engineered the factory flashing protocol for the newer Honda ECUs to flash through the harness connector. To my knowledge, the ECUs previous to 2006 for the VFR800 do not use this protocol. "
The entire thread is here:
As many of you may have seen, we have been able to successfully reflash the 2010-13 VFR1200 (F & DCT models) with fantastic results. We have acquired an 2006-09 VFR800 ECU and have begun the process of disassembling the code. What We would like to know is: Who might be interested in having th...
www.vfrdiscussion.com
After all of that, I'm guessing that the 2003-2007 ECM is probably the "older" style and the 2008+ would be the newer style? Purely speculative on my part. But, if that's true, there's a possibility that the 2008+ could be flashed.