There are so many odd results, that it is difficult to know if there is a primary issue (wiring, assembly, settings, etc) that is responsible for some or all of them. If faced with diagnosing this vehicle, I would back-up and begin basic testing of the Mega, the PCB, verification of settings (ALL of them), then wiring, etc. Two sets of eyes are better than one.
Not to confuse or add to the pile, but have you verified some basic stuff like which coil pins are for what? It is a passive ("dumb") coil, apparently with power, ground, and shield connections. Is the wiring correct? If not, the coils may not function correctly, and you may be sending large noise pulses through the vehicle, disrupting other functions. In a related question, have you tested for running EMR noise with an AM radio or o-scope?
Another possible issue is your ignition coil driver wiring, which may need the following changes to the Speeduino and added resistors to each driver channel. Again, these are not necessarily suggestions for primary causes, but possibly additional or contributing issues.
One example layout for firing quad waste-spark from one TC4424 driver channel. Ignore the cylinder assignments, as this was for a 16-spark-plug engine, but the concepts are the same. As the small resistors are to suppress harmonic ringing (rapid on/off oscillation) from each 211 input to others, they should be independent as-shown, rather that one resistor to feed all of them. R1-R4 can be 10 to 18 ohm 1/4W by the datasheets. Check the coil driver is on a good heat sink, and staying reasonably cool. :