A note about the two engines verses one discussion. During early development of OBDII engines, it became apparent that crankshaft rigidity was going to be a BIG concern for All Speed, All Load Misfire Detection. You see, a crankshaft doesn't actually revolve at fixed speed while at steady RPM. It actually accelerates and decelerates enough that we can calculate misfire by looking at Delta (change) of rotation at 36 points per revolution.
As the piston comes up on compression, the crank slows down (and speeds up during a power stroke)....and this happens for each cylinder in the cycle. Where it gets tricky is when the main bearings become worn, or the harmonic balancer starts to break up. Misfire detection becomes inaccurate. A flexible crank (or block) exacerbates the problem.
You'll also see misfire detected when wheel or road vibration is sufficient to alter crankshaft acceleration during power strokes (a harmonic feedback in the driveline, that matches firing frequency). That means the the power made by combustion (pressure, which should peak at 11-17 degrees after top dead center) was counteracted by external forces.
This may be the "AHA!" of twin engine arrangements. Feedback lash within the system is entirely capable of interfering with the peak pressure event. Remember....if your peak cylinder pressure occurs after about 17 degrees ATDC, the piston is running away from the gas expansion pressure and power falls off DRAMATICALLY. Note that peak piston acceleration occurs when the pin is about 90 degrees tangent to the crank center/rod angle, which is higher in the cylinder than we tend to believe.
Here's another consideration for twin engine synchronization....if the back lash reaction pressure occurs slightly before top dead center, and the spark event has occurred, the reduction of crankshaft rotation speed will allow cylinder pressure to climb (from BTDC combustion) while the piston is still on the compression stroke. That results in huge pressure BACK against the piston. The combustion event duration is dependant on timing and fuel vaporization/pressure. You can't push backwards against a rising piston without paying the price in lost power (I remember Bultacos that would run backwards with an unlucky kickstart). I had a Buell that could get hot, sneeze in traffic, and spin the rear tire backwards while I was going forward about 20MPH.....that was irritating!
I suspect the best solution is get as lean as possible (for quickest burn), use low 90% distillation temperature fuel, and get the timing as retarded as possible while seeking that 11-17 degree ATDC peak pressure. That should minimize the "synching" effect problems of twin engines. Too much focus on the downstroke of power can easily steer us away from the "pushback" of excessive spark advance and rich mixtures.
Fascinating problem, these twin engine machines! I'd love to build one just to try to learn more about it.
Regards, JimL .....see you at Speedweek (with my single engine bike).