Hi John:
Well if it was in a kit and you guys did the wiring harness, I would say that its the builder who should know or figure out the resistors for LEDs are standard practice. After all, the whole purpose of Experimental AB is to research and learn. In wiring, its always best to involve some experienced people. Many builders actually get the wiring done for them by facilities or avionics mechanics. I guess certain amount of experience or knowledge may be being assumed.
Here is a video from DigiKey also about the LED resistor needed for a given LED and how to get it. You do need to know the LED specs
But getting back to what your issue really is; I think the fact that there is a disconnect in CANBUS communication daisy chain before the termination. It would be some effort but not a lot to check that that the HIC A and HIC B pin outs from Rotax iS harness to your DB connector on miniDAQU from Kanardia are correct using a continuity check. Second one side of HIC A and HIC B are done by Rotax but the other side of the plug is done by the builder. If the pin outs are not carefully kept the same, you simply will not have any data passing from the ECU forward. Also the pins on Rotax $10 HIC connector are finicky. Without the right Molex tools that cost 100's of $$, you are unlikely to get good crimps and insertion of pins into the plug and that may also be an issue.
Basically I doubt the problem is that your LED lights are causing X on your Kanardia EMSIS EFIS and making your engine run rough.
The lights are just not correctly wired with resistors so their color and brightness are off and yes that should be corrected but it will still leave you with the problem. The problem is that your HIC wiring in CANBUS daisy chain has simply not been correct this whole time. That is what I suspect.