Hello Iwbs,
It seems you are still having some hardware issues, your spark events are causing noise on your secondary trigger. That said, does your board have the cam-hall inverter applied or not ?
I suspect you are firing in the wrong phase, so yes, cyl#1 spark lines up with tdc but in exhaust stroke, not compression stroke. Adjust your config accordingly so your cyl#1 spark lines up with cyl#1 in compression phase (offset 360 degrees by adjusting ign out rotation, triggertooth and tdc_delay) and you should be good to go.
Best regards, Dave