So I assume you have a KK/JTAG/RGH modded device such that you can run custom code (I doubt this is within the provisions of a map editor or save editor, disc swap might be a different matter but eh).
Usual progression with this sort of thing is work up the modification ladder.
Can you unpack and repack (no changes) and have it work.
Can you unpack and repack with a replaced file with said replaced file being another level (presumably all valid data in there) and have it still work.
Can you unpack and repack with an altered file that should still be within parameters as you can divine them by analysis and looking at other files. This ostensibly to see if there is a hash (the baseline mods should defeat system level and with those available it is rare to see devs opt for further, especially outside saves, but we have been surprised before) but can also dodge item and other memory/CPU/storage/... limiting options.
Larger changes. This can be more random approaches, or more informed (copy chunks from elsewhere, analysis as you imagine it to be by looking at the format and game in action, iterative approaches on data and seeing changes, disassembly driven, leaked data from whatever, sideways moves from PC where formats are known/level editors exist...)
Arbitrary changes as you desire them.
Wherever the crash comes in is where you start to fix things and move up from there.