The original setup for the 41 was for a 16k btu split system just to cool/heat the salon, and a second, smaller system split between the forward and master staterooms. I an quite surprised to hear that your one functional compressor is split between the salon and the master. Are you positive? Someone must have bubba-ized it because the salon needs the most cooling (dedicated 16k btu) and to split that with the master doesn't sound like they are matched and could be a problem. A 16k btu compressor cannot run a 16k btu AND a 8 k btu air handler properly. The A/C experts here can elaborate further. I believe the master has an 8k btu air handler and the forward stateroom has a 4k btu, both originally run off a 12k btu compressor which is a perfect match....
Hope this helps.