The game having open source is no help. Either you write native machine code or you're going to have a hard time doing much.
That said, I'm not sure how efficient other people's ports have been.
Cave Story could barely be backported onto the Sega Genesis
The Sega Genesis has a much weaker CPU.
One big issue would be the display. Some things to consider:
1) What's the point of porting Cave Story to this system, specifically? It's an entirely 2D game, what would you really get out of making it 3D? (see: shithouse NiCALiS ports)
2) The reduced colour count may mean that, combined with the faster CPU, the system could potentially actually run the game with enough optimisation. (although that's just in theory)
3) Do you really wanna play Cave Story with a monochrome display and superficial 3D effects?