It would probably be a good idea to get a voltmeter to see what is actually coming from the MH. From what you said, I would guess it was wired for a combined toad. That is what the converter on the MH is for. Once combined, the lights cannot be "uncombined". A converter (wired backward?) on the toad probably doesn't do anything good.
You could remove the converter on the MH and the toad and wire without any converters. You will need 6 diodes for this installation.
I suppose you could wire the toad as if it were combined and use the converter on the MH, but none on the toad. The brake lights on the toad would act as turn signals when operated from the MH. Do nothing to the wires for the turn signals on the toad. They should operate as normal when driving the toad, but not function when connected to the MH.
Roadmaster has some nice wiring diagrams (as supplied by eTrailer)