By that account it should run but I'm confused on your testing procedure. Toss out a few thoughts. I have had some issues with caps and rotors. I don't mix brands as some rotors are shorter then others. Another thing is the spark has to ground somewhere even while testing. If it doesn't fire at the plug it grounds somewhere even back to the ignition box and can kill it. 2 bad plug wires can do it. It still ran with the old distributor. I'd drop that back in and see it it starts. I'd still rock the engine back and forth to view timing chain slop. 1 tooth it would still run, but not want to take throttle under load, 2 teeth pretty much game over. I have seen them jump at shut down. And I would still pull the plug and verify that you're on the compression stroke with a thumb over the hole and line the balancer to zero. It's easy to get lost by just looking at the valves. Something is getting missed it seems.
