Am I understanding the circuit right? Q2 should always be high, except to trigger the spark right?
IF you are talking about Q2 on the timer board then no it should not be always high. its a npn transistor. meaning that a logic 1 turns it on which will cause the signal to the hv board to go low.
Has anyone checked that there is not excessive ripple in the hall signal
I have not checked, but seeing that the whole setup is powered from a battery pack I don't think there is a whole lot of ripple. I will continue to try and reproduce the problem. I only noticed the issue after I had to make changes to the spreadsheet.