Code not executing after flash- (LFCLK issue?)

[DW-AMM]

Hello I am trying to make a custom version of this boot loader for the nrf52840 BMD-340 module so I can run Arduino code on it. The boot loader runs successfully as I am getting correct blinking codes etc. However, when I program a blinky program onto it nothing happens. I believe this might be because the LFCLK source is set incorrectly to be external (which the BMD-440 doesn't have) when it needs to be the internal RC.

I am very new to bootloaders so I am unsure:
Can the boot loader setup the internal RC OSC for the application code?
Does the boot loader change the default clock source when exiting?
Does a configuration need to be changed somewhere else?
Does the Application code control the clock source?

Thanks for any help!