BA Jake has the better solution there.... if you can use the Woolich software package to disable the upper injectors (or bias them all the way down to zero...), then you can use what you have. The thing is: you'll still need to tune the thing for boost.... how do you plan to do that? By the time you're done paying for third party software and piggy back hardware to get MAP reference fueling adjustments you will be in nearly as much money as a good stand alone.... never mind boost control hardware/software and proper datalogging.... and most stand alone systems come fully featured; no gotchya money upgrades for quick shifters, pit speed limiters, datalogging, etc.
The gen 3 is damn near the same bike to the gen 2. The crank, cam, stator, Reg/Rectifier, temp sensors are all the same. The relay box covers the same functions as well. IF (big if) you wanted to do an electronics swap from gen-to-gen the EASY way, you would need the Relay box, ECU, wiring harness, and throttle body(s) assembly, and there would likely be a bit of changing pigtail ends on random things at worst (such as the lights and fans and such). Someone who knows what they are doing could simply re-pin your existing harness to work with gen 2 ECU and throttle bodies, but I would consider that to be an advanced job for the average person, and requires a lot of thought. Sights like this one: https://www.corsa-technic.com/
sell most of the connector ends and pins for doing jobs like that. And after all that, you'd have to come up with the software and/or additional hardware to tune the new ECU set-up.
It's all easy to me at this point. AND it's still a huge job. Not a boast, just trying to give you the facts... it's easy to confuse complexity with difficulty. If you do half-ass/corner cutting/hokey adapting on a turbo conversion you are going to melt all sorts of stuff, over and over again, until you give up or end up doing it right.... ask me how I know. If that's the road you want to go down to learn, by all means do it; you'll never get any better knowledge than the hard earned type! :)