After tweaking the host, access and error logs seem to be back after a week. Surprise, surprise. We will see.
Lots of time updating, refining, inline documentation for the Fan and FanLab modules. Now that I think I understand how they are supposed to work I can start evaluating why they don't seem to work.
Troubleshooting/documenting the fan software has revealed:
When the processor is idling, clock frequency drops to the minimum, 600MHz. With my library FanLib this turns on the fan - unnecessarily. When I start traffic between the RPi to the laptop the clock returns to max, 1500MHz and the fan is turned off. The assumption was that when the cpu over heats, the OS would reduce the clock frequency to reduce the heat. I didn't think about a reduced clock during idle time.
When troubleshooting the temperature was ~60.374°C, ~140°F, well below the 80°C, 176°F, ON_threshold. At least we know the clock freq preempt function works without having to force a change in clock speed.
The control button interrupt isn't working. Could still be a (plug) wiring issue.
Sphinx seems to be doing odd things with constants, #: tags. Question to the "community."
The Mineral Spirits track cleaning and NO OX ID "A Special" track protection process seems to work. Trains run fine - for now. Longitudinal testing will take longer to see if this procedure is better i.e. last longer. See videos (long) and where I got mine.