Has anyone taken calls on this job prior to you getting stuck with it? I can't recall if the CIR relays you mention are akin to those stupid Midtex plastic encapsulated type that Amtech used, but if they are, and some one has taken trouble calls on this unit just before lucky you, I'd bet somewhere one or more of those little teenie weenie flimsy contact pins has been bent over, compounding the original trouble. This controller uses 1s, 2s, 3s etc. for floor position? If so, I'd also be looking there.
