I have owned both the D and AF-S versions of the Nikon 300mm F4, used both with a kenko 1.4 tc, and the AFS version is much faster focusing. If you get the nikon 14e II AFS, as I did, the focusing is super fast, and the images made me very happy.
I had the same issue with the 80-400vr, and found that at 400mm the images often turned out soft, so switched to the faster and sharper 300mm afs prime. I did not particularly like the 300mm non-afs F4, heavy, akward for manual focusing, and perhaps just a tad faster focusing than the 80-400, when using a 1.4tc.
BUT, the expense of these lenses had me selling them all and going with the Sigma 400mm APO's, both macro and non-macro versions. These lenses are much cheaper than the nikkors, and produce very sharp images. It seems to me the contrast in color is not quite what the nikkor's are, but I'm in the process of comparing over the next couple days.
If I could have justified the expense, I would have kept the 300mm afs f4 with the 14eII tc, but having used the sigma 400mm primes with similar results, I opted to sell that stuff (around $1300usd used--paid around $900usd by fishing on ebay) and get the sigma 400mm macro apo for around $400usd.
Hope that helps. Oh, and I really liked the 80-400vr overall for image quality, but again, the expense... I'm on the lookout for inexpensive used copies, but they are hard to come by. Same for the 300mm afs.
Oh, and I have used these lense on both my D50 and D200. The d200 was faster of course, but the afsF4 w/tc14II still focused very quickly in the D50.