Compression significantly different between throttle open and closed…why?

I would first attempt the compression test in the same way you did and see if you get the same results. Second I have another question,  is the F1 a US market bike with a vacuum petcock? If yes then I would check the petcock for a leak in the diaphragm as have read where this can lead to a leak into the #2 carb via the vacuum hose/port into the carb and cylinder creating a flooding so to speak into that cylinder which will keep it from firing correctly. 

Thanks everyone for the insights. I’ll try the wet compression test and see if that changed much. 

@gd4now I do have the vacuum petcock, although I bought a cheap aftermarket one recently. I will admit that I have to run it on prime or else it doesn’t get enough fuel for the 3 working cylinders…

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......or/and maybe the synchronization is not great, and the butterfly of #2 is almost closed...with not throttle, related to the others.

I'm thinking the same thing, 

"Compression significanty different between throttle open and closed…why?" 
Same reason it's harder to breathe through a straw than it is through a drainpipe. 

wrote:

Thanks everyone for the insights. I’ll try the wet compression test and see if that changed much. 

@gd4now I do have the vacuum petcock, although I bought a cheap aftermarket one recently. I will admit that I have to run it on prime or else it doesn’t get enough fuel for the 3 working cylinders…

Is the vacuum line from the petcock connected to the problem cylinder? Perhaps the diaphragm in the petcock is leaking badly.

Ok so I was about to do the wet test but I ended up with the following numbers, cold, throttle closed:

1: 135
2: 145
3: 140
4: 155

…so I figured things are good? 

I then thought that maybe I should double check carb vacuum balance. Vacuum was too low (~10cmHg) so I adjusted everything up to in spec. 

Still no fire in cylinder #2 and that’s while using an aux gas supply and the vacuum petcock port capped

I can’t figure this thing out

You need three things for combustion....compression, spark and fuel.  If compression is OK, and I would use the standard test with the throttle open, then check for spark.  If you have spark then the problem is fuel.  

I have always heard that just because a plug sparks outside an engine. does not mean it is sparking inside, under compression.
What is the best way to tell if a plug is firing?

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I have always heard that just because a plug sparks outside an engine. does not mean it is sparking inside, under compression.
What is the best way to tell if a plug is firing?

Swop it with a good cylinder and see if the problem moves with it 

^this I would like to know. I just switched out the ignition coil (and wires and caps) on that side hoping to resolve something. I have a hunch there still might be issues with the points/condensers 

wrote:

^this I would like to know. I just switched out the ignition coil (and wires and caps) on that side hoping to resolve something. I have a hunch there still might be issues with the points/condensers 

Are you absolutely sure the high tension leads are connected to the correct cylinders? One coil fires cylinders 1 & 4, while the other fires 2 & 3.

Yeah that’s how it’s set up.

update: I’ve got 13.3V at the battery. Voltage at the ignition coil leads are both 11.7. Is that normal? That doesn’t explain why one cylinder isn’t firing but I thought they should be at or near battery voltage

edit: if both ignition coils are unplugged from their leads, they will read the correct voltage. I don’t understand why it would make a difference