Yeah go ahead and check the fluid in your master cylinder and bleed it again.

But I think that your transmission fluid could be causing these shifting problems also. All though mobil 1 synth is some good stuff I highly recomend Honda MTF. You can get it from your dealer. Your transmission and more importantly your synchros need an oil of just the rite viscosity to function properly and the synthetic mtf could be throughing off your synchros just a little bit, and be causing your shifts to mabye feel "notchier".