If you download the Rotax 912 Heavy Maintenance Manual and look at section 74 you will see that there are 4 things common to cylinders 3 & 4:
1. The pick-up coil on the back of the engine. Measure it resistance at the ignition module plug. Check the gap from the flywheel.
2. The ignition module. Swap with the other module to see if that fixes it.
3. Some of the wiring. A combination of visual inspection and resistive measurement should prove that it is OK.
4. The coil. Unlikely that this has failed and is more difficult to test. You can measure the resistance of the primary and secondary windings but this is not a guarantee that all is well.
I've listed them in order of likelihood. Good luck, and let us know what you find.
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