And where is it that you're going to get these "Higher Output Aftermarket Alternator Components? Seems to me that I've seen several posts on Wanting a better charging system for the 550s and, to my recollection, nobody has any answers. I believe that the "Better Charging System" with or without going to fuel injection. I mean, if improving the lighting on the bike taxes the charging system, then that should be the area that needs tending to first. Just my opinion, and some others. If you're seriously thinking about fuel injection, you should also do some improving on the motor itself (intake, cam and exhaust). Won't do much good to shove the fuel mixture in, if it can be taken care of efficiently and gotten rid of effectively, you know? I have to go with Geeto & MRjeck's comments.
Later on, Bill
I've seen aftermarket charging systems for the 650/750 models, but haven't really looked for parts for the 550. It's all about how much you want to spend on the parts. You can buy a $220 stator and $400 rotor from online retailers that claim 400 clean watts out, which is about 30 amps. Plenty to run these bikes with a computer controller.
I also agree that you would want to build the engine to take advantage of the injection system. I plan on (within the next 10 years

) building a SOHC4 utilizing fast burn technology and computer controll components. I've already emailed Larry Windmer (
www.theoldone.com)... He builds engines that make 1hp/cc. I won't be getting that much out of an old SOHC (being air-cooled, and would blow head gaskets and heads) but 1/4 hp/cc should be possible.
The injection would be required to make the full throttle range usefull throughout the entire RPM band. Megasquirt's can be programed for highway cruising mileage, as well as WOT (18:1 A/F ratio at cruise, 14.7:1 under moderate acceleration, and 12:1 at WOT). I'd use a MAF sensor, MAP sensor, knock sensor, and wideband O2 sensor.
Here's a video with a DOHC CB900 FI'd. Watch the throttle response.
I just got rid of my 2003 ultra glide with efi. I had a 2-1 header, cams and the harley race tuner for the efi in the bike. It was a nightmare, I never did get that pos to run right. I was happy to get back to carbs, even though 4 carbs are a real pita to tune also. But at least I don't have to take it to a shop that charges $55 an hour to work on it. If I could leave something stock it would solve alot of my problems, but that would be way to easy.
There's a difference, though. If you put a Megasquirt together you don't have to pay someone to work on it. You hook the thing up to your laptop and tune it yourself. The "stock" injection isn't really tuned to be the most efficient, anyway. You can easily get more power and more mileage if you tune it yourself with disregard to emissions, etc.
This guy used 2003 gsxr600 injection bodies on his 900F and a megasquirt. The subject is pretty interesting. Seems worth it.
http://cb1100f.net/modules.php?name=Forums&file=viewtopic&t=13119&postdays=0&postorder=asc&highlight=megasquirt&start=0