Nice Cafe you got going on Lordmember. You will most certainly need more charging capabilities with the added fuel pump, injectors, O2 sensor, etc. I've heard the SOHC 750 A's alternator puts out a bit more than the regular SOHC 750's?
If Strynboen can build you a bigger alternator I would take his offer. The LED's will help some, but unless you drive without a headlight the stock charging ststem will not keep up. After about a half hour of riding, the microsquirt will be leaning out your injectors due to not enough voltage...not a good thing! The bike will start and idle fine, but once you are over the 3/4 throttle you could have big problems. It's impossible to properly tune fuel injection with voltage drops.
I'm on my second Microsquirted fuel injected Honda. 1st. is a DOHC 750 turbocharged with Suzuiki GSXR700 throttle bodies. It would have been a lot easier to set-up and tune without the added boost problems. The 2nd one I'm working on now is a SOHC 750 automatic with a small supercharger and the same Suzuki GSXR 600 throttle bodies as you are using. I like the way you are running the throttle cable to the center bodies...I never thought about doing that.
Now Lordmember...when you get your Microsquirt and the wiring harness..you will look at all those wires and say some nasty words under your breath like I did. Here's the secret when it comes time to wire up the fuel injection part.
1: Completly finish all the stock wiring first eg; Lights, Starting, Charging, and Ignition.
2: Have all your injectors and sensors in place with their appropriate pigtails You probably know what sensors you need..if not...this is what you need (a): O2 {you need to weld in a bung before you put the exhaust back on} with provisions for a heated sensor or maybe an LC1 (b):Throttle position sensor (should be on the Suzuki bodies?) (c):MAP (manifold absolute pressure)..the Suzuki one will be fine if it's there? (d): CT (coolant temperature)..just stick the sensor end between the cylinder fins and make a bracket to hold in place. (e): IAT (intake air temperature) you can put this anywhere close to the throttle bodies inlet.
3: Mount the Microsquirt, fuses, and the 2? relays.
4: Now the real secret...do one wire from the microsquirt at a time...just like eating an elephant (one bite at a time!). You will find many wires that we don't need or use with a motorcycle engine...just cut them and seal the ends. Just make sure you get the different grounds in the right places and be careful with the sensor feed wires (they use a real low voltage from the Microsquirt ECM). Try your hardest to keep any of the Microsquirt wiring away from the ignition and charging wiring (it's very easy to pick up unwanted "noise" generated by the these components and could give you problems when it comes time to program).
I'll post some real good links for you when you are ready to set-up your fuel system.
Take care; Clifford