If I want to substitute the music tracks, what happens if they aren't the exact size of the originals when I go to write the disc? Will it just cut them off, or will it not burning correctly? If they are all longer, will it be OK as long as the total running time fits on the CD? If they have to be the exact size, how exact to they need to be? Can it be down to the second, or do I need to edit them to the exact frame/sample/whatever?
For most PCE/TG-16 games, the wave file must be exactly the same size as the original. You can replace them with whatever you want, BUT, you must make sure they come out to be the same exact bytes in size as the original. If you don't, the game will have problems. Many programmers hardcoded sector offsets to be used when it comes time to play an audio track, so if any of the wave files change in size and you burn a new disc, every audio track will get a new sector offset. This is bad... If you reduced in size say the 3rd audio track, every track file thereafter will have a lower offset. So when the game attempts to play any of those tracks, they'll begin playing some time later within the track, and not at the beginning. You get the idea.
Now, there are games like Ys IV where the game code was written to always fetch the sector offset (or rather, the LBA) directly from the TOC of the disc. For those games, you can resize the wave files and will not have any problems. But I don't know how many of them there are.
So basically, for most games, the answer is that resizing the wave files will cause problems such as lip syncing issues, music not starting correctly, crashes even, etc. But, there are some games where you can get away with it, as I mentioned, like Ys IV. You'll have to run tests on the particular game you're working on to see if it'll work...
Also, as was already pointed out, you can use my TocFixer tool to enforce the correct wave sizes after you make your replacements (assuming the music you use was made to be about the same length as the original). You can get it from my site as well, here:
http://www.ysutopia.net/index.php?ind=downloads&op=entry_view&iden=4Also, the cue file doesn't seem like it has very much information in it. For all the audio tracks it just says, "INDEX 01 00:00:00". Is that normal?
That's normal.
I see the .toc file is much more specific, but I'm pretty sure my CD software will ignore the .toc file.
The TOC file is in a format recognizable by the emulator PCEP for Sony's PSP system. That's mainly what you'll need it for (when using the /PCEP option), if not for TOC reference. If you're a casual gamer and not into any of the techy detail stuff, yeah, you can ignore it.