I'm trying to figure out where is the save file for ToG. I checked in the ...Tower of Guns\Binaries\Win32 folder, but the .Bin files aren't updating so I don't think those are the actual save files. Is there another location to check?

you need the gamestate.bin for your game saves and optionstate.bin for the options. Both should be in [...]\TowerofGuns\Binaries\Win32