@xusu
I had been planning to release a version of the program that exports one soundfont per track to help with this kind of things. One per track mainly because samples are tuned differently for every single tracks. I never really got around to it, since the whole thing is a broken mess really.
Don't use -gm. It won't work well with pmd2 since the tracks have several percussive tracks, and some just don't. GM expects track 10 to be drums always, GS doesn't. The game also never uses more than 16 tracks, so don't worry about it, the default mode will always have 16 tracks max. I think your problem with the chromatic/percussive tracks not switching modes properly comes from how the FL studio sequencer doesn't seems to handle importing/converting sysex midi messages. My tool puts in each midi file some sysex messages to tell the synth to run in GS mode, and set some tracks to chromatic/percussion tracks. A bunch of older synths, like windows' default built-in synth don't support that. So you'll probably have to change those things manually when you import it in FL studio since its midi import is far from perfect.
Also, I suggest you dump the raw pmd2 samples using this line :
"EoSRomRoot/data/SOUND/BGM/bgm.swd" "out_pmd2samples" -hexnum
And then export the list of sample used for each presets for each tracks:
-swdlpath "EoSRomRoot/data/SOUND/BGM/" "out_pmd2samples.txt" -listpres -hexnum
Then if you compare the cv_info file and the out_pmd2samples.txt files for each tracks you'll see what samples each track/instrument presets uses, and can listen to each individual samples exported from the soundfont. That's how I did to figure out what samples are what. It really helps a ton, since the game's soundtrack messes with the samples a lot with effects and etc.
For instance, in treasure town, if you listen to the samples you said are bagpipes, they don't sounds at all like bagpipes. The composer just layered several notes to sound like a bagpipe. But in other tracks, those very same samples are used for something that sounds closer to what sounds more like an English horn or something close to it, maybe a bassoon or some "non-standard" variation that sounds like that. The actual bagpipe samples are used in bgm134 and 137 for example.
Also, some of the instrument samples used in the game are instruments not in general midi or gs. Some percussion(like that Indian percussion in track#29), and etc.. So I put what was closest.
About your earlier questions:
1. About the cv_info file, to change the midi instrument used for a given in-game instrument/preset just set the number in-between the MIDIPreset tags to the preset number you want. Like:
<MIDIPreset>81</MIDIPreset>
You don't need to touch the DSE preset. The tags are explained at the top of the cv_info file too.
2. That's because of FL studio's Fruity LSD does not support GS sysex messages, or basically any sysex message afaik. Better use something more compatible like foobar2000 or the bassmidi driver, or anything based on fluidsynth to play the midi with a GS compatible soundfont and you'll notice the drum/chromatic tracks are fine.