With some more thinking and suggestions from a guy who turbo'd a streamliner K75 to 203mph at bonneville, I think I will just leave the ignition as-is. The bosch system is very good, and in his case worked to 12,500 rpm with a slight modification.
So right now I am looking at the following setup:
Stock:
-Coolant Temp Sensor
-Igniton System
-Injectors
-Fuel delivery system
New:
-Fan Control (Maybe). I could even set the fan to run for a minute after the bike has been running for 10. Would prevent any sort of fan seizure issues
-Fuel Control System
-Oxygen sensor (Narrowband for now, I'm to cheap to do a wideband system. Although this looks promising in its cheapness:
http://www.waltech.com/site/index.php/open-source-projects )
-Potential addition of a multi-function display: Fuel+ on steroids. Can do MPG, Estimated to empty, Temp, AFR, etc
-Manifold Absolute Pressure Sensor: (2x built into the MS system: one for automatic, constant barometric correction, the other for throttle body vacuum signal)
-Intake Air Temperature sensor: will use a GM coolant temp sensor, works the same, but with better durability, and sufficient response time for a naturally aspirated engine.
-Throttle Position Sensor (rather than an idle switch): I am using a cheap one off a hyundai: same fitment as one off of a volvo 850
-I may add an automatic fast idle stepper motor, to replace the fast idle cable. I figure I can do something more useful with the choke knob than to run the fast idle.
Will Remove:
-L-Jet System
-MAF sensor (I will keep it in a box, with everything needed to return to normal, L-jet system, ready to be overnighted if need be)
-Idle Switch