Okay! We're getting somewhere, maybe. I see that your FAST Neuron is on the latest firmware, 02.26, which is good. But also bad because if it was out of date, updating it is an easy way to solve problems :)
The FAST platform has an init_phase_1 handler to do a "soft-reset" of all the connections. There is a debug log when this happens that I don't see in your logs, but it's on the platform level rather than the neuron itself. So you should add debug: true to the root fast: config section as well as nested in the net: section, that would help.
The soft reset sends a command to each port of the FAST board and awaits the response, so if one of them is not responding that would cause the init_phase_1 to never complete, which is aligned with what you're seeing. And that's the only init_phase_1 event I see that's platform-based, so all the others would trigger on virtual mode.
So I think that's where the issue is. What the issue is still don't know. The logs don't show any commands going out to the FAST board to trigger the reset, which means it may be an MPF bug rather than an firmware issue (if MPF was sending a command and not receiving anything, that would cause the same hangup but we would see it in the log).
If the additional debug: true doesn't provide anything helpful, we can add more thorough debug logging to the flows to identify where it gets hung up (and fix it!). Sorry you're stuck in the process, getting the board up and flipping for the first time is a huge milestone and you're so close!
-Anthony