So I was playing around to see what the issue was with the flickering and it would seem (hopefully it's this, so that I can fix and move ahead) that my MCU is misbehaving. I isolated the various LED connections via the firmware, enabling one at a time, along with the BL to see what it was, and,
1. The RGB didn't have any effect on the BL - Pin B7
2. Indicator 1 (caps-lock) would cause BL to turn off when led was on - I've switched mine to pin B4 on my PCB. Originally it is on pin C6.
3. Indicator 2 (caps-lock) would cause BL to flicker when led was on - Pin D7
4. Indicator 3 (caps-lock) didn't have any effect - Pin F1
5. Capslock LED indicator didn't have any effect - Pin C7
6. Backlight LEDs are connected to Pin B5. BL was not enabled in the firmware on the github repo, I enabled it on my system. However, the BL are not responding to toggle, step commands. I used hid_listen to check and the command seems to be going through, so no issues with the keymapping.
I've attached a hex file along with the keymap, if someone could test this please, it would be highly appreciated. I've mapped Indicator 1 to C6 as per the original PCB.