Your tracker.cfg looks ok, you should try refreshing the databases the proper way (you don't need to reboot phone to apply tracker settings). If you like command line do:
tracker-processes -r
/usr/lib/tracker/trackerd &

If you want a GUI I have written one that is in extras-devel called tracker-cfg.

And yes, the entire MyDocs directory is indexed, this is because it counts as a removable device.