If you really, really want to remake JJ1 with HD graphics, I'd suggest fiddling with programs such as Game Maker or Clickteam Fusion first. Both of those have been the technical foundation for various succesful 2D indie games on Steam.

For EarthBound 64, I know little about it. If there was a prototype ROM there is no more reason to publish it now than there was back then. Starting a fangame project from scratch may be less work than finding out how to hack a broken prototype.