Bump, i took a look at FCEUX and PGO'd it, in addition to trying out GCC 9.1 along with it.
SMB3 now runs at 50 FPS with no overclocking (360Mhz) and when overclocked at 456Mhz, it manages to hit 60 FPS consistently.
I may try out other emulators again as a result (probably Oswan or Temper) but for now i think this will do for most NES games.
Just overclock it and you should be fine.
Grab the new OPK in the first post.