I picked up the Japanese version a few weeks ago and I've noticed quite a few version differences so I thought I'd post my finds here. Might be a bit wordy. If I have something wrong it's because I haven't played through 100% on English and I used a guide for the most part.
1. Japanese text is a lot faster than English
2. The pirate ship password is in Japanese (thankfully they're in hiragana so they were pretty easy to record). I compiled them into a list here along with what rows/position for each character.
http://pastebin.com/2Pi2J9WT3. It is quite well known that the heart piece at the bottom of savage labyrinth is under grandma's house in JP, but there's also 2 more I found that were changed.
a. Planting 14 flowers and talking to the guy on the bench gives you 100 rupees (you spend 140 on them...) and the chest that appears after lighting the lighthouse at windfall also contains rupees instead of a heart piece.
b. Instead, one is on one of the small islands around forest haven. You climb up to where you would normally go to the nintendo gallery but you climb up a bit higher and exit on the opposite side, set the wind SE, then leaf glide to it. Treasure chart 3(?) is here on English
Other one is in the center of horseshoe island where normally treasure chart 28(?) is.
4. The Japanese version has some rupee locations missing. Notably the "101 rupee trick" does not work because...they're not there. There are also not any pots around some of the triforce chart locations (e.g. islet of steel). I've been farming the ghost ship, killing the 2 poes and wizrobe, collecting 311ish rupees and then savewarping to repeat.
5. Triforce chart 5 is not what is pulled up after sinking the golden ship, instead treasure chart 16 is obtained and it goes through a chain of charts to get the triforce chart itself (it goes 16 (shark island) to 28 (needle rock) to 3 (eastern fairy island) to 40 (headstone) where TC5 is gotten).
6. The cutscene for cutting down the barrier happens automatically on Japanese, on English it needs to be manually started by swinging the sword. (I played English for the first time in a while and ran straight into the barrier lol)
Will update more if I find some.