The 2009 Aprilia Tuono has a writeable ECU but you need the appropriate equipment from Aprilia in order to perform the task. AFAIK there are no aftermarket tools to replace the ECU programming equipment provided only to Aprilia dealerships.
As well, Aprilia recommends that you DO NOT put a piggyback ECU on it. It is one of the few manufacturers that actually puts out releases regarding this.
The reason surrounds how the piggyback reinterprets data coming from the various sensors. When the standard ECU says to the injector, put in more fuel the message is proxied to the through the piggyback ECU on it's way to the injector and modified due to the mapping. If the piggyback gives more fuel than the standard ECU ordered it will reflect in the 02 sensors and then the standard ECU will lean it out as a result and the piggyback will increase and you receive very choppy throttle response. An example would be driving down the freeway at constant speed and feeling the bike surging quickly over and over. It's very slight and very annoying and very tiresome on long rides.
Aprilia is next level in it's view of performance upgrades. They offer race wire harnesses, race valves, pistons, bodywork, Ohlins suspension kits and performance slip on and full race exhaust systems. All covered under warranty and all included in the OEM parts inventory.
They also make their ECU programmable to match the exhaust systems that are specifically designed for their motorcycles. Akrapovic is their exhaust partner, so it's great that you have an Akrapovic exhaust on that beast. It's the right one. I'm actually surprised you could source one for a 2009. I imagine you procured it from the UK or western Europe. They are all either titanium or carbon fiber. Only the best.
I hate to say this to you but....take it to the dealer. There is no other way unless you can somehow get your hands on the special ECU tool that costs upward for $3,000.
IF you procured the Akropovic from a dealership AND it's on the OEM race parts list they will usually flash your ECU with the matching map designed by Aprilia and Akropovic for no charge. Your profile says your in the desert. If that's Phoenix, look up the Aprilia dealership here, I know they do it for free. It's super quick. If they don't, probably 1 hour.
I just want to repeat, your boyfriend is right, it's to lean and needs more fuel.....but DO NOT buy a piggyback. Search out there on the interwebs and you will see the results of a piggy back.
Dynojet and Yoshimura claim they have resolved this piggyback issue but I can tell you from experience they have not. Yoshimura only offers for the RSV4, not the RSV so that rules them out anyway.
At the end of the day, it doesn't make sense to do the piggyback when you can just flash yours, aside from all of the potential issues.
Hope this helps.
Nice question. I'm shocked there was an Aprilia question that even showed up. It's a rare and beautiful bike. Once your ECU is flashed go out and rip a few stand up wheelies on it. The dry sump engine prevents the engine from eating itself up due to oil starvation! :)
Cheers AND..........Go Aprilia!