I'm really enjoying "lurking" in this forum and reading this thread in particular. Decided to register so I can participate.
I have a D7000 but ran into similar issues as the OP. Spot metering on something that seemed to be around 18% grey cleared up a lot of exposure problems and using spot focusing versus matrix got me MUCH more predictable results. I'm currently taking a digital camera class and of course all of the assignments are to be shot in full manual.
I'm still not to the point when I can take better pictures in manual than the D7000 takes in auto scene modes but I think I'm getting close. I'm currently shooting in jpeg mode and do very little post processing (using Gimp). I do plan to shoot RAW and to install Lightroom once I half way understand the basics.
I'm wondering is someone could have a look at the shots I took at
Travels with the Original Easyrider® Pictures from my PCC digital photography class for a little C&C. My goal right now is to get consistently good exposure and focus. I think I may be close but my technique probably still needs a little tweaking. Perhaps more than just a "little"
I'm also wondering why the color is noticeably better when I shoot in scene mode versus in manual, even when I use VERY similar ISO, shutter speed and aperture settings. The meta data looks pretty close except for white balance red, blue coefficients (whatever that is).
I was also completely unaware that even a really good (~$200) lens (mine is a Nikon 35mm 1.8) does not shoot very clearly above f11 or so or under 2.8. I've had a Pentax 35mm that I carried with a zoom lens exclusively for 40 years. This is my first time shooting with a prime and I've had to adjust my style significantly. However, I was under the impression that any good (DX) lens would shoot acceptable quality at any aperture setting, so long as the rules of DoF were observed. Perhaps it's because the D7000 is a REALLY good camera, but I started noticing the same problems with focus that the OP saw, as soon as I varied much past f5.6 - f11.
I'm too much of a noob to even know what I am asking for at this point. Perhaps some insight as to what I need to work on in order to get me to the next level of shooting ability.
Much obliged in advance!