The real value of the breadboard test system is that it enables you to find/discover things that were not so obvious.
Currently I have the Start & Stop buttons wired to the Arduino. I also have all six of the Low Pass Filter relays enabling circuits installed and today I installed and used LED16 which is the circuit that must be engaged to sense the TR signal from the transceiver. Spent a little time getting LED16 to work properly as I had a bad relay.
Then I decided to use the actual 48 VDC power supply in place of the floor fan connected to the hockey pucks. The supply came on as desired when you punch Key #1 and does go off when you punch the 2 or 3 or 0 Keys. BUT I find that the going “off” condition does not happen instantly. The 48 VDC holds for a second or two and then slowly drifts down to 0 volts. That means the amp could be smoked by the time it gets to 0 volts.
More details at N6QW Homebrew Radio blog.