I spend way more time over on ZX-14ninjaforums than here lately but here's what i have been learning about flash v modules. I'm sure much of it all applies to the busa same as the 14.
Flash is EVERYthing your ECU is programmed to control. Mainly we are talking flies, fueling and perhaps timing. There are more functions like Top speed limiter, rev limit, cooling fans.....etc. When you are talking engine tuning, its mainly AFR, Timing and Flies.
First off, flies. There are secondary flies that restrict air intake and do not permit full power at lower rpm. The secondaries are controlled by the ECU. Then there are the primary flies that are the same thing as the secondary flappers but the primaries are controlled by you. You would like to have no secondary flies but you cannot remove secondary flies from a busa and have it run optimally. I've heard of people doing it but the word was that the bike will run best with flies in and flash to change what rpm/gear the flies open. I'm still unclear why you cannot simply take the flies right out and have full control of the throttle with the primaries but I'm just recalling what i was told some years back. You have to tune flies and that means flash. There is no module to tune flies that I'm aware of. Once flashed, the ECU encoding is changed from Suzuki encoding to Woolich encoding forever. You can flash back to stock values but it will be in Woolich language. Your warranty is voided. You can get a different ECU that has not been flashed to solve that problem.
Next AFR. Ever see a fuel table? It is a grid with cross referencing boxes for rpm and throttle position. You have a number in each box (or "cell" as they are commonly referred to). This number indicates the amount of fuel to be delivered at X rpm and Y throttle position. So when you flash, you change the fuel numbers programmed in the ECU to optimize the power output of the engine. The kind of exhaust and possibly other mods may have a significant effect on your fueling requirements. Your engine is also one of a kind. It has unique fueling requirements that are a little different than every other busa engine in the world. The elevation you ride at has an impact on the fueling requirements (unless the busa has an o2 sensor and I think it does but only on the stock exhaust). So you see, you can send your ECU in and have it flashed but it will be a flash for the tuners busa with the tuners mods, not your busa. A good tuner will look for AFR mapping that will match your bike/mods as closely as possible. However, if you want the flash that's best for your bike, you have to bring your whole bike in and have a custom tune done on a dyno. You can use modules to adjust the stock values or flash that custom tune to your ECU. Again, the ECU cannot be returned to stock format. If you want stock AFR again, you can have it but it will have to be reflashed in Woolich format or you use modules to adjust the flash to stock (which sounds downright confusing to me).
Last, ignition timing. Timing is controlled through a very similar table as the AFR is. Each cell has a number that tells the spark plugs when to fire in relationship to the position of the piston on the compression stroke. The value in the cell would dictate X° crankshaft rotation at Y rpm and Z tp. The guy I talk to seems to leave the ignition timing at stock values in the ECU and control timing via an ignition control module such as the SB6 or DynoJet Ignition Module. There are no more SB6s out there. The DJ module will work with the PCV but it will not work with a Bazzaz fuel module. SO we are stuck if we have Bazzaz fueling. If you want to play with timing, you REALLY better ask a lot of questions from people you trust, know what you're doing and don't mess up or it could very well be bye-bye busa. Sorry, I can't advise on that as I am just getting into all of this self tuning business myself.
So if you have a PCV, you have taken the correct first step. You can control your fueling just as well as a flash would have but you will not alter your ECU one bit. You can try different fuel maps and see what works best. Now add DJ AutoTune-200 and POD 300. You got the world by the ass, baby! ....if you are willing to hold the throttle WOT and top out in 5th or 6th gear and then let go to 0% tp, you can do everything a tuner would do with AFR on the dyno. Last, add the Ignition Module V and now you have control over timing, just be careful about what you do with it.
Only thing not addressed is the flies, rev limiter, cooling fans and whatever else the flash does. You want that don't you? Well, you will have to flash then. Keep the modules though. Remember, the flash is a flash for the tuners busa, not your busa. Your knowledge of self tuning will allow you to adjust the flash so it is perfect. There is nothing inherently better about a flash. Don't buy that BS about the signal needing to travel a longer distance by interfacing with modules. We're talking the speed of light through those wires. two feet means zip.
.....or just get a flash and call it a day. All depends on how much time and $$$ you want to spend on this crap. You could go all the way to getting your own Woolich software. Buy your own dyno! LOL
Oh, BTW....you made the right first choice on the bike too. The busa is still unbeaten in my book. Watch out for the Gen3 ZX-14RR when we get it some day. Hope they update the busa to match or beat it. I'll buy a new bike for sure.
Daron