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I was exploring the save file structure, and I discovered that at least for the inventory items, the structure is simple. In the savedata folder you have dp.sav. If you open that up in a hex editor, the inventory items for toolbox are listed roughly in the region of B890-BA00 simply as numbers of how many each you have. I was mainly interested in giving late-game weapons to play around with, and here are addresses I discovered:

B8F8 - infinite axe
B908 - light sword
B920 - guitar
B924 - infinite assault rifle
B928 - infinite revolver
B930 - Wesley Special
B934 - infinite rocket launcher

Just edit the save file for any of the above addresses to read 01, and you will find the item in your toolbox.