Both cameras have great features.
The D90, among other things shoots in full HD at cinema 24fps where as the D5000 shots at 720p.
Both have Live View but only the D5000 has a tilt/swivel screen.
Both cameras have a metal chassis but the D5000 is physically smaller than the D90.
If you can, try both cameras at a demo area and see which one feels better in YOUR hands. You cant go wrong with either one.

For nature shooting go with the 70-300mm and maybe add a teleconverter. This would double the power of the lens with only reducing it by 2 f-stops. Thus giving you a 140-600mm lens.

There are standalone miniDV decks that can be left attached to your computer at all times. Some are just decks and some have a LCD screen for viewing.
The stand alone decks can be pretty pricey for just a play/recorder unit. The large screen being what drives the price up.
What you may want to consider is a lower end camcorder you can leave attached to the computer just as an input/output unit. This way you'll still have your main camcorder to shoot with and you'll have a small monitor to view what to capture to the computer.

All Digital-SLR cameras have what could be called a Point-n-Shoot mode. In full auto mode the camera will make all settings for you...ISO, Focus, Shutter, Aperture and use of Flash will be done automatically.