A new dc-dc converter would be cheaper and easier than a new controller I guess. I'm not sure if there would be any reliability issues with running the stock controller at 36v. The LVC wouldn't be at the right level, so you would need to watch the pack voltage but that's easy enough.
Do you know what the max current drain on the 12v system is? A good dc-dc converter in that range should be pretty cheap.
"One test is worth a thousand opinions"