If I run it without the coil firing it all works fine, its just with the coil in circuit I can scope the noise spikes.
I was wondering if I could decouple (capacitors) the serial port somehow
Actually, its the TC4424EPA that's missing a required decoupling (bypass) capacitor. This could be the main problem.
Overall, all the 100K pulldown resistors seem weak, I think it would be better to use 10K on the MCU side of the circuit. However, this probably isn't directly related to your problem.
I would configure all unused pins with the internal pullups enabled.
The A4988 stepper driver circuit seems incomplete ... no capacitors?
Might need to add opto-isolation to the Ignitor circuit inputs, however, maybe first of all overall grounding could be improved and/or placing your circuit in an EMI/RFI protective case, or adding ferrite core(s) to the power supply connections would help.