It would be really nice to have a running bike to get all the signals from, especially the ignition system. It can be a rising-edge or falling edge, have different number of teeth in the tone wheel, etc. It's always nice to have an oscilloscope to grab this info on a running system before removing it. You mention ignition coils "with one common wire between the two", do you know what this is? Having a wiring diagram from the service manual would certainly help figuring out how things are configured.
Some items that jumped out at me:
Intake air pressure sensors: You mentioned that there is one per cylinder. I've seen that but not worked on it before. My Hayabusa had four pressure taps (one for each cylinder) that went to a single sensor, which sort of "averaged" the manifold pressure for you. With individual sensors, a generic system like MegaSquirt is going to have a hard time determining what manifold pressure really is (it's all over the place on an individual-runner basis). You'd have to either put a restriction in with a large volume behind it (mechanical filter) or put the manifold pressure filtering WAY up on the electronic side. They both have unpleasant side effects in system reaction time. Factory ecu's for applications like this usually have a "windowing" strategy where they sample manifold pressure only during a certain crank angle or time. The other option (not my favorite by any stretch) is run an "Alpha-n" system with throttle position and engine speed as inputs and use the pressure sensor to correct for barometric pressure. You typically have to resort to this when you have a car engine with a huge camshaft that gives poor pressure signals at idle. It's sensitive to so many things, which is why I don't like using it unless I have to.
Do you have mechanical throttle on this or is that electronic as well?
Gear indicator sensor: I don't recall MegaSquirt having the ability to use different ignition or fuel maps based on a gear, only the clutch switch being true or false. Not sure if it's just that my knowledge is slightly out of date or not.
Cooling fan relay: Probably what I would consider the "biggest miss" from the systems I worked on. There wasn't a way to trigger cooling fans using the MegaSquirt ECU. At least when I was building them. I used a series of relays to get the fan to work when the A/C was on, low speed when the coolant was warm and high speed when it was hot. It will be more simple in your case, with no A/C and just a fan on/off setup. I'd just use a temperature switch on the output of the radiator with a temperature you feel comfortable with (110C or something) connected to the ground of the fan. Do yourself a favor and put a diode going backwards from after the relay to the B+ side so when the relay lets go, the voltage spike goes back into the overall system instead of frying the relay. You can add a manual switch on the ground wire as well for an over-ride.
Air injection solenoid: Same thing as the cooling fan. Not sure the system has the ability to do anything with these.
I remember talk of a "General Purpose Input/Output" or GPIO daughter board around the time life got in the way of my projects. It looked a bit "Russian farmer" for me. You had to remove one cover and it sort of stuck out into the wind. Maybe they've enhanced that since I was last working on things. It's possible they've written some cooling fan and air injection features into the code by now.
You must have a lot more spare time than I do, this is going to be quite a project.
