If you put the $1000+ savings away for 3 years you will be have enough to buy a replacement body that far exceeds those sold in those $2300 packages.
As for the two bodies you were considering, both accept VR lenses, as do all current Nikon bodies (well, not sure about the latest version of the FM ("Fully Mechanical" film body) - it's just that a DX lens is designed to only cover the smaller DX-series sensors and won't cover the larger sensor of the full frame models. All older lenses will work with current digital camera, but, as said by MajorChode, some bodies are more compatible with older lenses than others in the sense that some functions, notably metering, might be lost with some bodies. I recently chose an older model D80 because it retains metering and autofocus with all AIS and later lenses, pricier models added features I didn't need, and the huge price jump to get a FX (full frame) digital body wasn't an option I could justify.
I would do an inventory of the lenses now owned, and check the specifications provided at
http://www.dpreview.com/reviews/specs/Nikon/ for the various models to see which lenses will work and retain whatever exposure metering and autofocus capabilities they had with older film backs.
One factor to consider in choosing a DX body vs. one with an FX sensor, apart from price, is that the effective focal length of the older lenses are effectively multiplied by 1.5. For telephotos, this is nice, since an 80-200 becomes 120 to 300mm, while for wide angles it degrades their capability, turning a 35mm into a 52mm. So if spouse really dug using a super-wide angle, you'd need to add in the price of replacement for that 16mm or 24mm lens, but the long telephoto lenses would get the equivalent of a free upgrade.
(The types of electrical and mechanical couplings between the body and lenses have changed over time. I think autofocusing on older lenses was driven by a motor in the body and a mechanical coupling while newer lenses put the motor on the lens and send instructions via an electronic connection, and such, and such as.... The D80 seemed designed to work with both, but some other models only worked with newer lenses.)
Or a gift certificate with a promise to help sort through the maze of details, with the $1000 held in reserve for the time if/when a newer body seems to be a good idea.
(edit to add a couple words)