I feel your frustration. The wiring that came with the Isuzu frame I have under my skoolie had amber directionals and red stop and 4 way flashers. I used a converter so I could use the single (dual filament) stop/directional/tail lamps on the bus body which works fine. Unfortunately I then had to figure a way to wire a toad requiring the amber/red system from the bus. Going from the original Isuzu wiring to the toad should have worked but instead it produced results like yours on the bus!?!
I eventually got the three systems to play nice with each other by using a half a dozen 5 terminal 12v relays in the toad. As the previous reply suggested, how about showing us a wiring diagram and explaining exactly what you want to accomplish----it can't be rocket science if I managed to figure it out but I'll be happy to share my .02 cents worth if you wish.
Jack