You probably checked for this, but I thought I's mention it. Any chance that the manifold runner itself is cracked, and sucking in huge amounts of air?

I had one other thought, seems a longshot, but you seem to have covered all of the other bases.

What would happen if the exhaust sequence on that cylinder was not operating properly? A faulty exhaust, either at the valve or a blockage in the exhaust manifold runner, would trap exhaust in the combustion chamber. After the firing stroke, the exhaust would have no place to go on the upstroke. On the intake stroke, no fuel/air would be drawn into through the intake - no place to put it. the compression stroke would compress the exhasut trapped in the cylinder, and there would be nothing combustible to fire at the top of the stroke.

That would also explain the compression test - the cylinder would continue to compress the same trapped exhasut.

What would cause this? I assume that when you checked the operation of the #3 intake valve, you also observed the exhaust valve operation. So, any chance that the encounter with the branches you mentioned in the original post wrenched the exhaust system, and somehow caused a blockage in the #3 exhaust runner?

Mind, this is only a theory, but you seem to have exhausted (pun intended) the other posssibilities.