My first post so be gentle
Having read 90% of this thread the bit that did it for me was:
You could just ignore all of this and place everything into the MyDocs/SimCity4/Plugins directory. If you do however, and then decide to use the Lot editor, or the BAT tool, or the PlugInManager tool (PIM) then having everything in the one folder will really confuse you and also not enable you to do troubleshooting if you should need to. If you only play the game it won't make a significant difference.
So if you've no intention of making or editing Lots, BATs or whatever and just want to play the game then basically just ignore everything else and stick the wole lot in the MyDocs/Plugin directory. Okay so the directory will get messy... just don't look at it and anyway, the game won't care.