I have everything installed/wired. I wanted to test everything to ensure it's operational before cleaning up the wires and reinstalling everything. At the moment, the front seat is out, the connections for the hazard light switch and airbag "display" (just above the hazard switch), and all the 12VDC/USB/HDMI are disconnected.

When I reconnected the battery terminals and try to go into accessory mode, I get the green light on the start button flashing, and a series of beeps. Is this due to the connections that I've disconnected?

 

Yes, the USB, HDMI 12VDC plug panel has a connector for a receiver device (antenna basically) to detect the key fob. With that disconnected the car will not start at all. You need to reconnect it before you can proceed. Common issue, most people don't realize when they start pulling connectors.