One of your problems is that the matte screen in your camera (this is what you are actually looking at through the viewfinder, it's a semi-transparent plastic screen that sits at the top of the mirror-house, below the prism housing) is designed to give a nice bright useable image through a slow autofocus lens such as your average f/3.5-5.6 consumer zoom. This is good if you are using a consumer zoom, but very bad if you are trying to focus a fast prime lens. The reason is that the extra screen brightness is bought at the expense of focus accuracy - is unable to show you the small depth of field at larger apertures than about f/2.8-ish. In other words, if you look at the image from an f/1.4 lens through this matte screen, the depth of field you see will be that of f/2.8 and not f/1.4. Again, for a consumer zoom this is entirely irrelevant but for a fast prime it is highly misleading. You physically cannot focus a fast prime accurately through such a matte screen; you are just not getting the information needed.

A solution for manual focusing is to replace the default "fast" matte screen with an old-school, coarse-grained one which will show you accurate depth of field for a faster lens, and more "pop" when things come into focus. You may also get a screen with a split-prism center, or one with a prism-ring round the center.

I'm not sure if Nikon offers such alternative mattes for the D90 but third parties might although installation is likey to be a bit more fiddly in that case. The downsides to a coarse-grained matte screen is that it affects light-metering, and that the view from lenses slower than about f/2.8 will be darker (much darker, in the case of an f/5.6 lens) in the viewfinder. The matte does not affect autofocus performance in any way though.