If I'm understanding correctly, you want a full frame replacement for the 17-55/2.8 zoom. There are numerous lenses that could work for you, including all those mentioned. My preference would be the 24-85VR for the focal length range and the useful VR feature. The lens does have terrible distortion but that is easily corrected in post processing or by shooting JPEG. You may not even notice it, depending on subject matter. I also like the 35-70/2.8D. It has a limited zoom range but it's a better built lens and the images are superb. It's also heavy and the combination of the D3 and the 35-70 may be too much of a good thing.
But I really prefer the 50mm suggestion. Between the ƒ/1.8 and ƒ1.4 Nikkor AFS G lenses, I much prefer the 1.4 lens. Either will do but the ƒ1.4 just has a better tonality to my eyes. The ƒ/1.8 images were a bit flat in comparison. Just my opinion, I have no objective evidence to back up my view. If you do go the 50mm route, you might want to invest in a second lens that you could carry easily to back up the 50mm--a 35 or 28 would be ideal.
And I have to disagree with Ian concerning manual focusing with the D3. I've been using AI and AI-S Nikkors with my D3 bodies recently and it's not that difficult, especially with the confirmation dot. It takes some practice (lots of practice if you've only used AF for the last few years like I have) but it's not impossible.
The D3 is my second most favorite Nikon, the number one being the D700. And the D700 is the D3's baby brother.