I'd like to take more than 999 images with the intervalometer, and I'm wondering if there's any trick to get past the 999 image limit. It looks like there's a
now setting and a
later setting--maybe I can use both?
You would need to use an external intervalometer to get where you want to go. That said, unless you can control the lighting, you would probably want something that can modify the exposure over time. (The alternative would be to put the camera into an auto mode and live with the inconsistencies. There would be a lot of manual correction involved frame-by-frame in creating a time lapse film.) That may mean that your D700 is not a suitable camera for the job, I'm afraid. (And I say that as a Nikonian.)
Somewhere back in the mists of time, Nikon decided to put its shutters under exclusively digital control. For normal photography, this has no untoward side effects. The only people who get burned by that decision are time-lapse photographers using ambient light exposure. The simplest way to do smoothly-varying exposures over time is to cheat by using the camera's BULB mode and varying the amount of time that the virtual shutter button remains pressed. The technique is called "bulb ramping", and this is where that digital shutter decision bites you. The time that a Nikon shutter can remain open is only controllable in discrete steps, even in BULB mode. In the ordinary use of BULB mode (making very long exposures), the fact that there may be a difference between what you do manually and what the camera actually does of a few tens of microseconds makes no difference at all to the exposure. So it's 240.000080 seconds instead of 240 seconds exactly. Big deal. But when you're cheating—using BULB mode to control the shutter into the fractions of seconds—it suddenly becomes a big deal. Your smoothly-varying exposure doesn't vary smoothly, it "jumps". I am aware of one means of overcoming that to a degree—an Arduino-based bulb ramping intervalometer coupled with a set of auto-created XMP files to smooth out the jumps—but if it exists in commercial form, I haven't found it. Again, if you can control the lighting, it's not an issue.
Canon, on the other hand, affords very direct electrical control of the shutter in BULB mode, and there are a bunch of effective bulb ramping intervalometers available for it (notable the Little Bramper). If you need to do an outdoor ambient-light time lapse, there may not be anything truly suitable and readily-available outside of the Canon world.
Maybe I'm not understanding, but I think you can.
The intervalometer allows you to specify when to start, the interval for shooting, how many intervals, and how many shots per interval. So, lets say the interval is 1 hour and you choose 99 intervals with 100 shots per interval, it should give you 9900 images.
Of course, there are a number of physical issues to overcome such as storage media, battery life, etc.
Am I missing something beyond that? I didn't see a cap of 999 there except for the number of images per folder (and 999 folders and 9999 images overall).