Hi @VolcanicCheese
1. Run code in RAM in the MCUXPresso IDE
Answer: Please use the following configuration:

Select the Link application to RAM, then your code will run in debug mode, even you work in serial download mode, I have tested it, and confirm serial download mode, the RAM debug is OK.
2. I was not sure where in the example SDK project I am supposed to write the fuse map address and write value
Answer: You are right, EXAMPLE_OCOTP_SHADOW_REGISTER_READ_WRITE_ENABLE is used to control the write code, as you know, fuse is one time operation, it just can be modify from 0 to 1, and can't write back. So, to the SDK code, it is very careful, and don't want the customer write the fuse directly, so it just give a fuse read version.
When customer need to write the fuse, customer can set
#define EXAMPLE_OCOTP_SHADOW_REGISTER_READ_WRITE_ENABLE 1U.
You also need to double check the fuse address, which is the correct address area.
To be honesty, to the new user, normally, I don't recommend customer operate the fuse, but your customer board situation is special, you didn't leave the GPIO for the BOOT_CFG.
Wish it helps you!
Best Regards,
Kerry