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Iv got several old Nikkor super-telephoto's and they all are excellent on
the D3. The Nikkor 600 5.6 ED-IF is a really sharp lens(with good tech). I know a pretty famous Canadian wild life photographer(Whayne Lynch sp) used one back in the film days. I would grab a used TC-14B which will give you a 840 mm F 8 . The great thing about the 600 5.6 ED-IF is very light, thin(except for the end) and well balenced and only 200 grams more than the 300 2.8 ED-IF AIS. Dont worry about the 5.6 f/stop with the D3 veiwfinder and the high ISO manual focusing will be easy with some practice. Good luck with your choice. I really hope you get it, I know you will love it.
I shot one just last week on a D300. It is a damn fine lens, as long as you can focus it. It's also incredibly small compared to the 600/f4 and 400/f2.8 AFS lenses. It's about half the weight of the 600/f4 AFS II, almost three inches shorter, and more than inch smaller in diameter. That's a BIG difference! If you can focus it for the subjects you want to shoot, it's a great lens. We were hand-holding it at ISO 1600 and 3200 and got great shots of a resident pair of red-shouldered hawks.
I have the AIS-n version (that was the last incarnation) which is slightly different then the AI version. Great lens if you have enough light, and far more portable then my other super-teles. The only issue you may run across, espcially on DX cameras, is some color fringing (CA). Nothing terrible, but still there, especially on white birds etc.
I got mine in pretty rough cosmetic shape (great optically however) for about $1000, 2-3 years ago.