That's a great question. Many people have PMed and asked this question. I'm not an expert on this, but I'll explain what I do know. If anyone else has more info please feel free to correct me. Also the Bazzaz website is a good source for info.
This bike has both the Bazzaz fuel controller (BAZZAZ Z-fi) AND the Bazzaz Z-AFM auto tune. These are two different modules that work together. The Bazzaz Z-AFM plugs directly into the Z-fi and uses a Bosch wide band O2 sensor in place of the factory O2 sensor. This is why you must weld in a larger bung into your exhaust when using this setup. Because you unplug the factory sensor and no longer use it, it throws the check engine light on the factory computer. The Bazzaz Z-fi is over riding the factory computer to control the engine, that's why each item you unplug to install it, such as the fuel injector nozzle for example, the bazzaz computer has control over how long it stays open or closed no matter what the factory computer is telling it to do.
You don't need the Z-AFM for the bike to run, it just makes it much easier to determine what the suggested air fuel ratios should be for the bike, especially for someone who has little to no experience tuning. When I finished installing all the upgrades to this engine I ran the bike on the learn settings for about 20 min. It ran like crap! During this time you run at all different RPMs in each gear. Once your done you come home and plug in the laptop and it tells you what the computer thinks you should set your map at. You simply click ok and save it. From that moment on I went to test ride again and it was amazing. It was smooth in all throttle ranges and I have never messed with it again.
I have a little over $2000 in receipts just in all the parts for this setup. (stroker kit, exhaust, intake, heavy duty clutch, lightened primary gear, Bazzaz stuff, etc) Stock engines are selling on ebay for 1000-1500. I am asking $1500 for the complete setup plus shipping. This engine still has very low miles on it and will be a plug and play for anyone who wants it. This is less than half what it would cost anyone to do this. It's a pretty simple swap, much less work that splitting a case to install a crankshaft. When I pull this engine out next week I'll make a video on how to do it step by step. Hope this helps guys.