Just wondering if the MISTer FPGA is an accepted platform for emulation?

If it's not listed in the Rules, it's not allowed. Only allowed Emus are FCEUX, Nestopia, Bizhawk, OpenEMU and MesenRTA.

It is something we probably should consider, we just haven't haven't had many requests for this. I do know it's becoming more popular though.

I may get with you to ask some questions, gather some data, etc. since I know you're pretty knowledgeable about it. We keep the accepted list of platforms/emulators fairly short due to the level of optimization this game has where individual frames are significant.