Looked into it. Haven't launched the game (my video card is broken), but the tool seems to be working fine. You just have to add the files you modified instead of all the previously extracted files. The tool is kind of dumb as the archive format is very simple - it just appends the modified file to the already existing data.pak and modifies the offsetpointer to that file inside the archive - which should work just fine as I dont see any checksums inside. This is why your data.pak doubled in size - you appended its contents to itself, which probably broke the tool and/or the archive.
Do it like this: create a new folder "pak", place the paktool.exe and the modified files (only those, not all of them!) you extracted from the data.pak. Also, place the data.pak inside that directory. Run the paktool: "paktool.exe /p data.pak <path to your pak folder>". Now the data.pak in that folder is modified. Move it back to your BS3 folder and run the game - it should work.
Good luck.
