Hi there Rabite890, Special, and chillyfeez!
Thanks for all of your comments and suggestions!
Rabite890, like Special and chillyfeez said, to release a separate version or patch to strip out the story will be quite an undertaking ... not a particularly difficult one, but would take a lot of work to strip everything out. You can always fast-forward the story sections using emulators as suggested by Special.
Regarding a separate patch for toggle to run, I myself actually prefer chillyfeez's 1st version of the toggle to run also.
However, for the sake of the general audience, the hold Y to run is much more accessible as I've had many people reached out to me before about a run function(because the toggle L while standing still to run was somewhat hard to figure out if you don't read the readme or the in-game training room). So with all that said, releasing 2 separate patches in the future for both versions of the run function wouldn't be out of the question!