It seems to me that all you really need in terms of new cables to put in two 6V batteries is a new ground point on the trailer frame near the far battery. One of the existing interconnect cables would go from the battery to the new ground lug, and the other would be the series connection between the two 6V batteries.
The only exception I can think of where this would be troublesome is if there's an ammeter shunt in the ground lead, in which case the shunt probably would best be moved and the sense wires extended. The existing ground cable could be abandoned or perhaps tied to the trailer tongue at a convenient place if the frame conductivity is somewhat lacking.