So I just bought a GTR is that what you guys call them? I want the GTR to be as powerful as my ZX [...]I REEEALLY HOPE I DIDN'T MAKE A MISTAKE...
Congrats. The Concours is better than the ZX-14 in just about every way.... except acceleration/power. If that is your primary objective, you have made a huge mistake and will never be happy. Just read this entire thread. The Concours engine was designed for more low end power, less vibration and noise, and more reliability. You cannot get the same power out of the Concours engine by replacing the exhaust, flashing the ECU, replacing the headers, etc. It would require practically rebuilding the entire thing, probably costing more than both bikes combined.
The Concours is plenty powerful for most people. And with some relatively simple and reasonable cost mods, you can take it to the next level. But that level is not ZX level.
Like are the throttle bodies the same... I don't know.
Perhaps you should have found out before buying one. No, they are not the same. Neither are the pistons, the head, the cams, the intake, the exhaust, etc.
What or how, or why did they de-tune the motor?
Read this thread first.
And what do I need to do the bring it back...
It is not "detuned" and it is not "bringing it back". It is designed for specific goals for sports touring... and it is the best in its class.
I need to lower the rear end at least 3 inches
Not possible, there is not enough clearance. 1" is the maximum safe lowering.