1) for those who have upgraded >from a D7000 to a D600, is there anything about the D600 that >you don't like as well as on the D7000 (AF point coverage, for >instance)?
Whilst the AF point coverage to me is the the main step back from my D700 in practice I've not found it to be a problem. I tend to focus and recompose in single shot mode anyway and in continuous servo I tend to use back button AF on, 9 point dynamic and lock on with the centre focus point. It works for what I do but then I'm not a full on sports or wildlife guy
2) Is the high ISO noise performance of the D600 >hugely better than on the D7000?
This is one area where the D600 is massively better IMO. With the D7000 I'd shoot up to ISO 1600 then spend a while balancing noise reduction and sharpening in Lightroom. With the D600 those shots need little or no extra work at ISO3200 and I'll happily shoot at ISO6400.
3) Do the larger NEF files of >the D600 slow down your workflow measurably?
On the D7000 the RAW files are around 20mb as opposed to 30mb on the D600. I have a quad core Mac Pro with 12gb RAM and Lightroom is not noticeably slower. A lesser workstation or laptop might prove a bit more sluggish when editing files. Without a doubt I'd use a USB 3.0 or Firewire 800 card reader - that will make a massive difference in import times and preview rendering regardless of system.
4) For >photography that doesn't need extreme telephoto lenses (like >birding), do you miss the extra reach of DX? Thanks for your >help.
This really depends on what lenses you have a what you like to shoot so it's very subjective. You could keep your D90 for backup and to use as a teleconverter (that's the main role of my D7000 second body now)
Finally, you mention you have DX and FX lenses and depending on the mix you have making the leap to FX can be more or less problematic