Just uploaded a new version (Beta 5.3). It contains a few small bugfixes, but mainly some graphical improvement. Most importantly, the Dragonite on the titlescreen has been revamped and all Pokemon Overworld Sprites have a proper palette and walking animations now!
Mew can be caught in the patch of grass on New Island, its like a game of hide and seek. Clefable evolves with a moon stone, yes. Wild Clefairy can carry one, there is one on New Island, one on Route J and 2 on Pinkan Island (If I remember correctly). Waterfall as a field move is removed on purpose, you can't climb waterfalls in Orange Islands.
I played the 4.2 version (my bad) on the arcade games website before learning through the 3 guards at Drake's island that version 4.2 is up to that point. Upon downloading 5.4 I went back to the arcade website where I found the game and attempted to load the new version (as I would a game I saved to continue my progress later) but nothing happened. Is this because this game in its updated form is not available on the arcade website? I know you suggest we start from scratch but it would be great if I could translate my progress to the 5.4 version. Do let me know what you think I should do at your convenience!