Keep in mind the ZX9's still in bits... and, as a measure of my commitment to the method, I *won't* be sticking the cams back in with the #4 cylinder cam lobes pointing outwards...
Just a gedank experiment not something I'm about to start advocating as a technique for the shed... thinking that, since the ignition system takes its cue directly from the crank, and since, on remote coil systems, at least. cylinders #1 and #4, and #2 and #3, spark from the exact same discharge, it's hard to see how the spark on one revolution of the crank will differ from the spark on the next... it's still the same coil driving the spark, powered by a discharge triggered by the exact same spoke on the ignition trigger passing a Hall sensor...
(pause)
...I just remembered your bikes run *points*, not CDI or TDI... at which point my familiarity with how it all works goes decidedly wobbly.
Could that be what's happening here? I'm thinking Hall-sensor-triggered ignition, you're thinking points?
Fundamentally, though, what I was getting at originally is that, with the crank at #1/4 TDC, the cams can go in so that either the #1 or the #4 cylinder is at compression and there shouldn't be any valve-piston clash.
This is how I've been learning about this stuff ever since I got into bikes... by posing dumb suggestions in public and being corrected.