There shouldn't be any reason for the boom ball valves not to function if you removed the accuboom harness from the boom cables on the rear.
Maybe AgLeader should not be selling you something they don't know how to make work on that machine.

I have to wonder why you are installing a direct command and adding switches to a cab already completely wired. Also note that the Case factory wiring was designed specifically for Raven controllers. The Viper was a factory option and still is today.