Yes indeed, there is no use in even connecting power to the fuel and ignition systems until trigger signal(s) and sync are OK. A few other comments:
1) Let's confirm you have cylinder #1 connected to spark/fuel drivers A, #6=B, #3=C, #2=D, #5=E, and #4=F; for your 1-6-3-2-5-4 firing order.
2) Some people prefer carb-cleaner instead of starting-fluid, feel it is less hazardous. You do not have to spray while cranking, you can be a long way away from the "danger zone"!
3) If it is firing back into the intake, then you either have a problem with valve timing/condition or improper ignition timing. Since it appears your sync isn't good, it is almost certain it is just the "improper ignition timing"...
4) I can appreciate that you want to use the stock trigger systems, but if you find yourself getting unduly frustrated trying to get this project going, you might want to consider scabbing-on a simpler "missing-tooth" crank wheel (like 60-2 or 36-1). Using that and your existing sequential ignition/injector wiring you could get it up-and-running on wasted-spark and semi-sequential fuel. Once there, then add in the cam signal for sequential, and then go back to the OEM crank trigger when you know all else is OK.
Edit: Lower the "cranking advance" from 10 deg to 0. That way no chance ignition will be too early. As soon as the engine fires advance table takes over.