G2 Throttle Tamer & PCIII combo on 07 - Excellent!

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The ECU is no way interchangeable between the Gen 2 and Gen 3.
Are the wiring harnesses different?
That I cannot answer, but the wiring harness is not going to be the only issue.

A brief and probably incomplete list of reasons the Gen2 and Gen3 are not interchangeable:

The Gen3 has:

2 ride modes, Sport and Touring.

Traction Control

Cruise Control

Throttle by wire

The Gen2 is not set up for any of that and the cost of retrofitting would be ridiculous. Why would anyone want to do this anyway?

 
Don't bother JUST changing the throttle pulley. Keep a sharp eye out for an '08 - '10 used throttle body. You won't regret it.
Were the throttle bodies really different? How about the 11-12? I thought that only the pulley profile changed and maybe the fuel map.
The '06 and '07 FJRs had a different throttle body cam profile from all other years, the profile on the throttle tube (hand grip) was the same. Changing the throttle tube cam profile with a G2 (or DIY as some of us have done) is an attempt to compensate for the abrupt throttle body cam.

Changing the throttle body cam would be a better solution, unfortunately it is not available from Yamaha as a separate item, and the whole throttle body assembly costs an arm and a leg.

 
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