And I was in firmware recovery mode since I started the router with the reset button held in and the power LED was slowly flashing, correct?
Correct.
And when I ftp-ed the trx file to the router, even though the file transfer was done in 11s, I was in a non-interactive reflash which means I needed to wait a long time before restarting?
The upload copies the firmware to a temporary file inside the router. Once that's done, the router starts the process of (slowly) reading that file, and writing it to the flash partition. That part can take a good 5-15 mins on modern routers, and up to 40 mins on the older N16/N66.
Just let it sit there, once the actual flash process is done, the router will reboot itself. You will now by the wireless leds being back on (assuming wireless wasn't previously disabled).
If you do update through the CFE mini website, take the opportunity to select the option to erase the nvram while at it.
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