39F040 PLCC32

To programm the 39F040 PLCC32 flashrom you need:

SNES maskrom flash adapter PCB
PLCC32 to DIP 32 adapter: https://www.aliexpress.com/item/32824998509.html

First you need to setup the Cartridge Reader Shield's config switches like so.

Then insert the 39F040 flashrom into the PLCC32 adapter and plug the PLCC32 adapter into the SNES maskrom flash adapter, make sure to leave the two top rows empty, and finally plug the maskrom adapter into the cart reader's SNES slot.
The two SMD switches don't matter in this case as they're only for the SOP44 slot on the backside.

39f040plcc32

In the main menu first select "Flashrom Programmer" and then choose "PLCC32 to SNES". To program the flashrom you need to erase it, then do the blankcheck and finally select write to flash it with your rom.
While writing a rom to the flashrom the led should blink constantly until the flashing process is completed.