1-Welcome to the forum. There is a thread here for "show us your vintage carbon" or something like that.
2-I won't put a value on it. Nothing personal, but there's a value inquiry thread for that.
3-Based on the condition and components, whatever you spend on upgrades would be a waste of money, and mostly for vanity.
4-Set up right, these can be very smooth, or very harsh. My guess is smooth enough, but could be improved.
5-You are not going to get a better shifting system than that 9-sp Dura Ace.

My recommendation list, and really none of these are needed:
A-Swap in a carbon seat post, pick a saddle that your body likes. The ride can be smoother.
B-Drop the wired computer/eyesore. At minimum, pick up a lower end Garmin 200/210 and get rid of the wires.
C-White wheels: American Classic Sprint 350's, perhaps the Aero 3 420 (a bit stiffer, sacrificing smoothness).
D-FSA SL-K crank set with the BB386 bb, silver rings. (would ruin the group "totality," but would work).

I can say this, giving an educated opinion, because I've built and ridden several of those.

My "worst" was a 15.1 lb build for someone else, full carbon everywhere and extremely stiff and light tubulars. Very light, very fast, very stiff, and I hated it. I built it on request, rode it once for 35 miles, and hated it. No relaxation.

My "best" was actually not mine, or even my idea, but the identical frame, carbon seat post, American Classic Sprint 350's, 10-sp 105 shifters, 7800 FD/RD (no better than the 9-sp DA), and a carbon crank set, FSA Wing bars. It is just under 18lbs, but probably as smooth and as sweet a ride as I've been on, period. I think the combination of the wheel set, drive train, and cockpit just worked. My friend owns it and knows it. Of course, I have a standing offer in case he ever decides to go insane.

I don't want to be harsh, but if it fits, you'd be foolish to do much to it. You can get lighter bikes, smoother bikes, newer bikes, but not much, and it will cost you. That group is beautiful and works great. There is a technological advantage to a newer crankset, but that's all. You may see a ride improvement with a carbon seat post, a saddle that fits, and different wheels, but only with certain wheels, the Ksyrium is an excellent wheel.

Trek retained Aegis Systems, Inc to help create a carbon frame set. Aegis did so, but a disagreement about how to do so arose among the Aegis designers/engineers. Some of them left chilly Maine for sunny California, to form Kestrel. Those left behind created beautiful carbon frames that were very aero for then and now, and very expensive, but with a lifetime warranty. The ones who departed found funding and created similar-looking Kestrel frames, I think beginning in 1986, that were quite similar in appearance to the Aegis. The forks and seat stays on the Aegis eventually became very bladed, and Aegis no longer makes frames; the Kestrels were pretty consistent for years, and were the better-known "milestone" carbon frames; the game changers. Several of Kestrel's models have become the Bike of the Year for some magazines, etc, and the RT series was known as one of the best values in an all-around bike for their era.

Not only was the 200 series an iconic design and promotion, the no-seat-post Airfoil, along with Trek's Y-Foil and Giant's MCR, a step outside the box, among the frames banned by the UCI for being "too much."

Good luck with that. It is a nice bike and a prime theft candidate.