You may know this already by virtue of using Nikon film bodies, but just in case..... The 'AF' lenses use the older generation AF system using a lug in the camera body to control the lens' focus. The current AF-S generation lenses use ring motors in the lens body itself - a great improvement in speed. The AF lenses are slower and seem to 'hunt' more than the new stuff, but otherwise they will work fine in the new DSLR bodies. Either system is dependent on the sophistication of the the camera's AF sensor system, with the high-dollar cameras having the better sensor arrays.
Neither AF system will work very well in really low light levels. Nikon claims that they won't work at all at effective apertures of 5.6 or smaller (not true), but that's just their way of avoiding complaints in that department. One thing that might help in these situations is to attach a modern speedlight like the SB-800. You can turn the flash head off, but it will still emit infrared light prior to shutter release to help the AF sensors out. The newest flash connector cord (SC-29 I think?) has it's own IR emitter that can add to what the flash puts out. I'm not sure if the cord's emitter will work with no flash attached. I could hook mine up and check if you want.
I'm not aware that an ED lens is better than any other in the AF department per se, but it may have some qualities that will indirectly affect the AF system. The AF system uses contrast as it's main measuring stick, so maybe the reduced reflections, etc of an ED helps in that department. Plus most ED lenses are on the higher end of the quality spectrum. I should point out that ED is a designation Nikon has used consistently to describe its 'extra-low dispersion' coatings. Although these coatings have gone through several generations of improvements, the ED designation has stayed the same.
I think you'll find that noise at low light levels is one of the Achilles heels of all digital sensors, regardless of brand. I've never used a D-200 so I can't help there. I have a D1H, D1X, D2H, and D2X and this low-level noise is a persistent issue. In my experience, the CCD sensors in the D1 series cameras is much better in this regard than the CMOS sensors in the D2 series. If I was going to concentrate on low light situations, I'd consider a used D1X over any of the newer models. It's a pro body with a 5.74 MP sensor, but it doesn't have some of the improvements in electronics of the newer models.
Other than that, I'd suggest a noise reducing software program. NeatImage is what I use and it works pretty well, although even it won't eliminate all the spurious white dots you get in a dark background from a CMOS sensor at 3200 ISO. NoiseNinja is another program that is pretty popular.
Hope this helps. I'm operating off the top of my head here, so anyone else feel free to correct me if I misstated anything.