Tom, the changes over the years are subtle but could be significant depending on the buyer. This link explains the primary ones:
http://performanceunlimited.com/supe.../features.html
More recent cars have reverted back to the original, one-piece windscreens (yes...makes parts availability for guys like me better!), a completely different differential (no more T-Bird based 8.8 IRS but still an IRS), and the engine bays have been adapted to accommodate the width of modular engines. There's even a little stretch in the vertical portion of the cowl (for more hood clearance) that is very subtle and can only be noticed when the car is lined up to an earlier model. I have #747 (built very early 2000) and I have noticed that the hood scoop on my car is slight lower than the newer cars (and, quite honestly, looks more in touch with photos that I have seen of original Cobras).
There was a range of earlier cars (can't recall the sequence off hand) that experienced a rear suspension bushing recall of sorts (mine included). In the annals of SPF builds, that incident and a batch of cracking windscreens or delamination problems ("bad glass" that seemed to crack when barely breathed on) have all been long remedied. Also expect the parking brake on #1050 to be mostly useless/non-functioning, as they are prone to get out of adjustment quite easily (that too has been remedied with the newer cars).
The good news is that the SPF dealer network has always stood behind these issues. Buying an older car may not necessarily afford you that same level of attention, but the dealers do want your parts business and they realize that, sooner or later, you'll end up upgrading and buying a new one. So they tend to treat us older owners quite well overall.
If you buy this particular car, join SCOF right away (a private Yahoo-based forum operated by an owner for the exclusive use of SPF owners). You can ask SPF-specific questions and other owners can offer helpful hints and possibly part # cross-references for most of the cars. "Blas" (CC and SCOF member) has also produced a wiring schematic for each "generation"...and it's priced very reasonably.
Good luck!
-Dean #747