Ok now that you have it as it is in the first screenshot, you need to merge the rest of the code manually. The easiest way to do this is to create an empty new project, import the latest tk2d in there, and then back in your old project, move all the files back to the default positions. Note: you MUST move these files from within the Unity project browser. Once you're happy all the files are back where they are supposed to be, import the new package in. This should overwrite all the old files instead of creating duplicates like it was the last time. I suggest keeping the standard directory structure, just to make upgrades easier.