Apologies for the delayed response (sinusitus is not fun!), but I really appreciate all the feedback received so far :) By knowing what's wrong, I can then make it right! ^^
To those having trouble with patching: There are several different versions of Pokemon Ruby (AXVE) out there in the ROM world, and I believe the specific variation you need for the game to patch properly is the oldest release (can't remember its specific number, but I'll research that when I'm not typing from an iPhone). If the ROM you have doesn't work, try another :)
To those having trouble with low health/running out of PP: There are healing berries, including Leppa Berries, scattered around the dungeons, but I can always add more ( that way, bad luck with traps is not the end of the world, as Long as you're dilligent in searching dungeons thoroughly (always talk to dead ends! Rocks and bushes like to hide stuff, too :) ). This is why I am not a good judge of the game's difficulty - I know where everything is. I can find all the items, hit the Uplift traps, and avoid the bad ones (mostly). ^^'
To those bothered by blood: It's supposed to be shocking because we don't expect it of Pokemon. The player is jolted out of a comfort zone, and the message comes across loud and clear: nothing - and indeed, no one - is sacred. NPCS, villains, and allies alike could all potentially feel the touch of death. This world is full of brutality, past and present - but also hope.
While I would be lying if I were to say there will be no more deaths in the game where blood is shed, it will only be used when important to the mood I hope to evoke in the player and the characters themselves. Ludicrous gibs it won't be.
To those with puzzle trouble: It's my policy not to give out answers (and I ask that others respect this within this thread itself - if you want to reveal answers, do it elsewhere XD ). However, a good hint is to always investigate things, even if they just seem like part of the dungeon's landscape. For example, "talk to" the pond in Tangle Thicket, and see if you can work out the rest of the puzzle :)
As of right now, the true alpha will contain:
More items, especially Leppa Berries
Proper respawning when you die ( the issue is there aren't enough flight positions in the game for every place you can die. I found a workaround, though, that well soon see :) )
Bug fixing (no more getting stuck in Golden Trail's puzzle room and stepping on mushrooms!)
More dungeons and more plot
Thanks so much to everyone! The feedback of both the positive and negative variety are what keep me going ^^