Sounds like you’ve checked a good portion of the items that might be at fault.
Based on what you’ve already tried and eliminated, I would move on to testing the fuel pressure to ensure proper pressure is reached and maintained. How were the results of the compression test and vacuum test? The only other items that come to mind are the gaskets for the intake and/or plenum possibly failing only for cylinder 3. Are the wire connector/pins and harness in good shape for cylinder 3 fuel injector and coil pack?
Normally a single cylinder misfire is a single point of failure, like a cracked piston or head or bad valve but you would have compression differences, a spark plug, coil pack, coil wires/connector, fuel injector, fuel injector wires/connector or an intake manifold or plenum gasket…