Initial Set up ploblems

Cube Orange w/ Herelink +
APM 2.0.27 on OS Catalina

I was having issues updating firmware as many people have been having. I loaded QGround Control up and update the firware there. Initially I was trying to install the PX4 stable firmware (1.10.1) which kept failing with the error
" Connected to bootloader:
Version: 5
Board ID: 140
Flash size: 1966080
Unable to find specified firmware for board type
Upgrade cancelled"

Instead, I choose Arducopter and updated to ChibiOS / Multirotor / 4.0.3

This one worked and I am now able to connect to APM Planner 2.0 and/or Qgroundcontrol however when I select ‘Update Firmware’ it does not detect the FC (it does when I’m on the main page, the orientation works,etc.)

In the Initial Setup tab, GPS calibration fails, I cannot select the type of craft it is and there are other little things that don’t work.

Where do I start with this?