for beginner, u shoot much better photo than me.
iso, aperture and shutter speed are the 3-brother that u have to master if u are into manual mode.
play around with spot focusing next, and spot metering to have a nice picture taken especially when the light is tricky
get a flashgun and try it out, personal choice, SB900, but now SB700 is quite reasonable.
go on with f2.8 fixed aperture lens, like those from Sigma or Tamron, of course original Nikon is the best.