To be sure, I replaced the rotor, leads and plugs on cylinder 3,4 (I reckon I can keep the old ones as spares). I also took out the leads to 3 and 4 and plugged in one of the old plugs. Both got spark, so I think we can rule out electrical issues.
I took off the valve cover to check the rocker assembly again. It looks good to me, except that the second last pushrod seems to be at a slightly wider angle from the rest:
Also, the nut second from the front is sitting higher on the bolt than the one second from the back. Could be that the bolts are different lengths. I made sure to tighten them to the same torque, starting in the middle. It looks level to my eye.
I made a video of the rockers moving while I turned the crankshaft manually. I can't see anything irregular, but I don't know what to look for or if it would be visible from the rocker assembly. I also couldn't feel anything that seemed strange while I turned it. There were periods where I could feel the compression (you can hear it in the video), and then it turned easier when it went to the exhaust phase (I presume).
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So what mechanical problems could prevent two of the cylinders from firing, and how can I check?