Hi Lisa:
Congrats on the new camera! (Hope to see it at our next Palo Alto coffee get-together!)
My take on VR/IS is from the Canon IS perspective, so I am not sure how much is relevant to Nikon's VR, but here goes.
IS is controlled by micro-motors and micro-gyros. As such, when they are spinning (on) they can impart some high-frequency vibrations to the camera. These are especially noticeable if the camera/lens is solidly mounted, like on a tripod, and Canon recomended with its early designs to turn IS off if you were using a tripod. Canon has alleviated this problem in its recent IS designs, allowing the system to sense it is on a tripod and turning itself off, but I don't know how Nikon handles that.
Thus, my IS/VR advice would be that if your lens is on a tripod and you are using relatively slow speeds, turn IS off. Though truth be told, I never bother since my IS lenses are the newer designs
Now for mirror lock-up. When I used to shoot Nikon (film cameras only) I noted that the mirror slap was most notable at 1/8th or 1/15th second, depending on the body. The negative effects of mirror slap tapered off as you went higher or lower, being essentially gone after 1/30th on the top end and gone by 1/2 sec at the low end. Interestingly, when I switched to Canon these parameters held, though now it seems the safe range is a little narrower being more like 1/30th and over and 1/4 or longer. You can easily test this with a moderate tele and your camera on your tripod.
So as a rule of thumb, I avoid 1/8th and 1/15th like the plague unless I use MLU. And typically, if I am on the pod and those speeds are even a possibility -- which often they are -- I'll use MLU as a matter of course.
Hope this helps,