Since it doesn't seem like anyone knows how the data is stored, here's a start:
Most *.bin files are archive files. They're similar to narc, but slightly different.
0x0-3: Unknown; 00 00 00 00
0x4-7: Number of Files
0x8-B: Start of 1st file
0xC-F: Length of 1st file
(8+8x) to (B+8x): Start of file index x
(C+8x) to (F+8x): Length of file index x
where x=0 to (value of 0x4-7) - 1
I might work on it more, but I'll give more time into my save editor for this game.
Have fun, ROM researchers!
[edit]
Attached simple .Net Framework 4.0 command line utility to extract files from a bin archive.
[edit 2]
An untested version for .Net Framework 2.0 has been uploaded.
Sky Rom Editor..zip
.Net 2.0 Sky Rom E.zip