I've been studying Japanese BA for the past few hours; here are my findings (I did all of my testing on Japanese
v1.0):
Here is the result of putting HSW into a bottle on the Bottle 1 slot (the FF's are not there naturally; I hacked them in to make it easier to see what values the HSW was writing). The first row is always XX 00 00 00 XX XX XX XX, just like in the US version. Though the last four XX's seem completely random, I detected a pattern in the very first XX; if you wait around, its value always seems to increase. I know it is
not linked to the in-game time, though, because playing the SoDT does not change it.
The second and third rows are also the same as in the US version; it's simply 00 00 00 00 70 17 00 00. The third row in the above picture looks different because I waited around before taking a screen-capture, which made the timer on the HSW count down.
The fourth row is something more interesting than the second and third rows. When you first catch the HSW, all eight bytes have a 00 value. However, when you press A to exit out of the text box, the last four numbers randomly change. When you dump the HSW, the numbers also randomly change.
The odd thing is that these results are not consistent among item slots. Here's what it looks like when you catch HSW in the Ocarina slot:
As you can see, this looks almost identical to American BA; it even has the lone 01 byte. Compare that to what it looks like when you put HSW into the Fierce Diety's Mask slot (trying to hack in FF's caused undesirable effects in the game):
There is neither a fourth row or a lone 01 byte. Even stranger, the first row always has a value of XX 00 20 00 XX XX XX XX, unlike the Ocarina and Bottle 1 slot above. Clearly, more testing is necessary to uncover the intricacies of Japanese BA, but I think this is a good start.
By the way, I think that the in-game timer exists as an unsigned long that begins at 00ADF1BC (as seen in the picture of the FD Slot BA). It's constantly increasing, it increases slower when you play ISoT, it jumps ahead when you play SoDT, and it pauses when you pull out the Ocarina, do Timestop, etc. What else could it be?