Gen 2 could take a while, its a whole new ballgame , way more complicated , apparently you get 1 chance to communicate with it before it locks up and only good for a bin...
Probably realy a couple of different levels you can use this reflash , no 1 would be buy or build a flasher like these
http://www.boostbysmith.com/ecu.html, and be able to do anything listed on the site
EG:
Ability to view all sensors data with a laptop connected
Ability to datalog all factory sensors on the motorcyle with a laptop connected for use in dyno tuning.
Ability to change fueling maps (both IAP and TPS maps), ram air compensation
Ability to change ignition maps (you can add timing in the lower gears like a TRE does without messing up your gear based fuel curves)
Increase your factory rev limiter (current software supports up to 11,650 RPM, more RPM is possible)
Remove the 6th gear speed restriction with the click of a button
Change ram air compensation based on your gearing
Compensate for larger fuel injectors needed for high hp applications
Compensate for increased fuel pressure needed for high hp applications
Increase ignition dwell time (turbo guys will like being able to open the plug gap back up some)
Disable IAT compensation for dyno testing
Turn your ECU into an ignition / fuel kill box for use with an air/co2 shifter
Control a shift light, or any RPM based output using the stock flapper valve circuit
Switch-able map selection for NOS, different turbo boost levels, fuel types etc
Share maps with people across the world and contribute to new exciting features constantly being introduced and implemented.
Now i could do any of this on your ecu or on a ecu i plan on having as a changover so no down time , but no point me mapping fuel and other specific to the bike stuff without your bike connected to the ecu and on a dyno...but anything not specific to your bikes needs like rev limit,6th gear speed restriction, put the ign retarded gears to a higher ign advance, compensation for larger injectors or higher fuel pressure, modify the flapper valve output for rpm based output,
How you may use these features is up to you,
You may want the features of a TRE but have a simple gear indicator operating too ,
I'm still trying to see how to use it to best advantage in my circumstances.