Nah, stock clocks. Pretty sure the HW is fine too, as I stuck RetroPie on a spare SD card and that runs like a champ.
It's just a file (or files) on the SD card in the printer that was causing it.
When I start Octoprint now, I see a list of files on the Pi and on the printer's SD. Before, I was only seeing files on the Pi... nothing from the printer. This would have been trying to get the file info on boot and had already started what would go on to kill my printer and crash OctoPrint shortly thereafter.
(Boot up, Get a list of files on printers SD... invalid character / contents or something... , maybe the printer or maybe OctoPrint could not interpret something to do with that file, tried and tried and some bug caused a crash / hang / kill after a few minutes of trying). Something like that.
The fact that I was trying to copy files to the SD card was largely irrelevant, but did actually accellerate that issue... though it would crash anyway after a mere couple of minutes.
Anyway, the copy to SD is now working successfully and I have stability (which is ultimately what I was looking for), though now I can see just how slow that copy is - I sadly won't be using it.