FI system overview
What follows is a general overview of the ins and outs (literally) of the FI system, and specifics on the ignition system. If you don't have a service manual, look in Helpful Topics for new 919 owners sticky at the top of the naked bikes section. Three up from the bottom of the Helpful How-To's section is a link to a wiring diagram which is actually easier to use than the one in the service manual when zoomed in: just place the cursor on the wire you want to trace and use the arrow keys to move the diagram around under it. Open a second window for the wiring diagram to follow along.
1 -- Power. The main power feed to the entire FI system begins at the starter relay, where the Red/Yellow wire connects directly to the battery connection at the relay. You can see this by removing the seat and looking at the right front corner: the connection is a single White connector with heavy gauge Red/Yellow wires in and out just behind the relay. From there it goes to the 20A PGM / fuel pump fuse in the fuse box. The fused Red/White wire then goes to the engine stop relay, which is powered by the kill switch and grounded by the bank angle sensor. From there all power wires to the FI system are Black/White.
2 -- Timing and synchronization. There are two sensors involved in this function: the crank angle sensor and the cam (miscalled TDC) sensor. The crank angle sensor is mounted on the clutch side of the engine and is comprised of a 12 pole wheel and a single magnetic pickup (to those in the know, it's a reluctor type) which sends a signal to the ECU. This provides a crankshaft position signal every 30 degrees which the ECU counts internal clock pulses between each crank sensor pulse to determine not only crank position within 1 degree, but also positive and negative acceleration rates, useful for ignition advance map addressing and injector open duration. Synchronization to TDC is provided by the cam sensor, located on the left side of the intake cam, which is a single reluctor pickup reading a 3 pole wheel: arbitrarily 1 pulse for cylinder 1 and two pulses for cylinders 4. A common misconception is that the cam sensor indicates TDC precisely: this is not the case. One of the crank wheel poles corresponds to TDC, and which one is registered by the ECU by watching the cam sensor signal, then using it to start looking for the proper crank pulse, usually 2 pulses after the advent of the cam pulse. This prevents shifting of the determined TDC position due to cam chain stretch and head gasket thickness variation, either of which changes the effective length of the tensioned side of the cam chain, and therefore the timing of the cam sensor signal. Once #1 TDC pole is determined it is used by the ECU to determine which ignition coil to trigger and when as well as which injectors to open and when. Cylinders 2&3 TDC is determined by the ECU by assigning the 6th pole of the crank wheel after the #1&4 pole. In this way, TDC for each cylinder is determined. None of these sensors is exclusive to cylinders 2&3, so cannot be the cause of your problem.
3 -- Injection. The injectors are individually triggered by the ECU corresponding to the intake strokes, but all are powered by the same Black/White power feed. Injectors 1&2 share a power line, #3 goes through the same connector but has its own power wire, and paradoxically #4 is hard wired directly to the ECU connector, so nothing is common to #2&3 except the same connector.
4 -- Ignition. The ignition timing is controlled by the ECU by addressing a map similar in nature to the injection map. Power is constantly applied to the coils through the Black/White wires. A very short time after a coil is triggered, a ground is applied to it by the ECU to reestablish a saturated magnetic field in the primary winding, which is maintained until the next trigger signal at which time the ground is removed, causing the magnetic field to collapse and inducing a short duration high voltage pulse from the secondary winding which jumps to the ground electrode of one plug to the cylinder head then to the other plug, which jumps to the center electrode and returns to the secondary winding, completing the circuit. If the voltage supplied to the coil is of insufficient current, the ground signal from the ECU is either shunted partially to ground by a short to a parallel load, absorbed by a corroded connection, or affected by a malfunctioning transistor in the ECU, then the magnetic field produced by the primary winding will not be of sufficient strength to induce a high enough current from the secondary winding to make strong enough spark to consistently ignite the air/fuel mixture in the cylinders, especially under heavier loads. In general, the higher the pressure in a cylinder the greater the spark intensity required to make a spark jump across the plug gap, which explains why removing one plug to check for spark is only useful to see if there is any spark at all, not to determine if it strong enough to light the fires under load.
Troubleshooting a weak ignition can be difficult without sophisticated equipment due to the very rapid nature of the signal to the coils, but some information can be gathered with a comparatively simple digital VOM with a 10 amp scale, a jumper wire, some dielectric grease (available at electronic parts stores), and some creativity. The first task is to visually check every connector associated with the ignition system one at a time by disconnecting them and inspecting for loose, bent, pushed back, or corroded pins. If they all look good, gently blow out any contamination, apply a generous amount of dielectric grease, and reconnect them making sure they are firmly seated and locked together. Remember to mark each connector as checked before moving on to the next one. Remember to check the ECU, battery, and grounds as well. Once this is done, move on to voltage checks. Before doing any voltage checks, pull the headlight and taillight fuses to minimize electrical load on the battery. First, check the voltage to the coils with the key on and the engine not running: it should show roughly battery voltage at both coils, and close to the same at both. Now start the engine and check voltage at the Yellow/Blue and Blue/Yellow wires. If there is a substantial difference, jump battery voltage directly to the Black/White wire of the coil with the lower reading. If the voltage rises to match the other coil, the power wire probably has some resistance in it, possibly in a splice inside the harness, and you will have to find out where this is happening and effect a cure. If the voltage does not come up, there may be resistance in the trigger wire between the coil and the ECU. In this case, jump from the coil to the ECU to see if the voltage matches the other. If so, fix the poor connection and you're golden. If not, there may be a problem with the ECU, and you may have to take it to a dealer for further work.
In any case, it is possible to fix most problems yourself if you are willing to be methodical.
Good luck, and post the results of your tests if you need more assistance.