Fletcher : I'm not really sure what you're looking for, if you understand the basics of fuel injection you'll realise that these engine are like any 4-stroke engine.
If you want to run with a 60-2 trigger, that's just fine if you do it right, i.e : wheel must be centered, correct trigger distance and properly shielded/grounded sensor.
With "missing-tooth" (60-2 wheel) you can then use any wasted spark coil packs to run the ignition, instead of wasting money on distributor parts.
What's important is that you build a solid trigger system that works with the ignition system you want to use. In order to get rid of the distributor you can either use wasted spark coils and a missing-tooth wheel, or run separate or wasted spark coils with a simple trigger on the crank (one tooth per TDC) and cam sync.
I have a configuration file of a late 1.1.7x firmware for such an engine which you can use to start yours with, but you have to setup and time the ignition because of your different trigger setup. These are the specs I have :
3.3 liter Boxer 6 cyl, ported heads, modified intake and exhaust manifold
Ignition systems uses three pcs of Mitsubishi waste spark coils.
Honeywell GT1 sensor on the crank with three teeth, TDC after the trigger is 90 degrees (it's ok with 10 degrees more than the highest advance you want to run).
Another GT1 sensor and one tooth on the cam shaft.
Fuel injectors are low-Z with power resistors, Delphi 65lb/683cc @3 bar
The only peculiar thing with Boxer engines is that you have to use the correct firing order and cylinder numbering. Rob pointed it out in another thread that it would also be useful to retard ignition and enrich the mixture in case the engine runs hot on the CLT sensor input, it might be available in the firmware some day.