Thanks for those pdfs gtrippleb, those are great!
I checked for voltage on those wire last night and didn't find any (with or without the lights on). Maybe the wire is terminated on the other end, or...
Another thought I had was the wiring was used for an accessory like cruise control, or it was specific to the Lx490x model such as control wires to the turbo's air heater relay. Yanmar may have used the same wiring harness on all three modes (Lx410x,450x,490x) to save costs and simplify inventory.