Does the five button Tstat still light up? If so it may be as simple as changing the dip switches on the Tstat. Here is a recent
post with a phone # of a guy that may be able to help if DougRainer does not chime in. After reading the OP's quote of $4,000 to change his system over I understand why you went with a non ducted unit. I was about to do the same on my Airstream, but he had a rebuilt board for that old Duo Therm unit.
I have three of the older Duo Therm units on my 04 Dynasty and even though they all work well, I've found a new, old stock unit as a replacement for $700 delivered that is compatible with the old CCC system. I believe in having spares and while $700 is not cheap insurance... it's better than $4,000+ to change to the new system.
*OP, this
trouble shooting guide may help.