If you are manually encrypting the bootloader then you have to flash it to 0x1000 and also create the secure boot digest and flash it to 0x0.

Not supported, risk of bricking devices, but technically possible. There are other posts in the forum about updating the partition table and bootloader via ota which would be required.

Apb clock is basically fixed to 80mhz. In the example the prescaler is set to 0 so each tick is 12.5ns.

It thinks the 2nd stage bootloader is 4mb so it takes too long to try and load it causing a wdt reset. This could be a bit error in flash read which when considering the baud rate issue may be due to unstable xtal clock or bad register value. If a hard reset fixes it then it implies something corrup...

You also have to burn and save a copy of the efuse secure boot key if you want to reflash signed and encrypted bootloader.

Yes reconfigure mux

No workaround for 34-39

Wrong forum, try https://bbs.espressif.com/

Also https://oshlab.com/esp8266-raspberry-pi-gpio-wifi/