@The Story - I really like it so far. It seems thought out, it's structured, and I don't even think I have anything to say as far as criticism is concerned. So far so good!
@The Happy Mask Shop - I'm not so sure about this as it is, only because it's incredibly vibrant and green. Considering that the tiles are already brilliantly vibrant but still somehow more subtle, it might be a bit offputting- right now. I think it'd be more accurate if I saw it in context.
On that note, the map looks great.
@Healing Spots - Well, think about it this way: In Ocarina of Time and occasionally in Majora's Mask, Great Fairies would often bestow power or items unto Link, healing him at the same time. On the same note, there were some that only healed him (and in the 2D games, there were only ones that healed him). So I suggest mixing the two. Why not use the healing ones as intermissionary healing spots between towns/routes/dungeons/etc. and and have the ones that bestow items/powers at significant locations?
...That said, an Inn would be a good idea for healing because it might be jarring if you go to a Fairy Fountain and BOOM, the Happy Mask Salesman is there playing his merry song. It might be more appropriate to have him in Inns. But I think, as far as paying tribute to the series is concerned, the Fairy Fountains healing would be the better route.