Man, I finally figured out where to go. I missed a fucking staircase in Shinjuku, lol! Because of all my wondering around aimlessly I've been completely annihilating main story bosses. Feels good to finally make some progress! =D
Seriously, the game really needs a patch for the automap. Displaying false information isn't fun at all.
I got used to it now but I lost at least 20 hours wondering aimlessly because of that.