Ahhh, I've got a 99 Concours with most of the farkles ever built. The bike did change a bit around 92 or so in regards to the front end, so with that in mind...A fork brace and new springs will help the handling quite a bit. A stage 1 jet kit will make cold starts easier and improve the low end on the bike. Since the front brakes on this bike are not what modern bikes enjoy, some braided brake lines and galfer pad or the like do help.
There are a number of convenience/comfort items too, like heated grips, a BMW outlet (or your preferred format) for the heated vest. Larry Buck makes large knobs for the screws on the side covers that allow you to access the rear suspension adjustment and air filter. BTW I've found that little preload in the front and maximum in the rear along with some air pressure seems to do best for me.
The number one farkle for your Concours is membership in the Concours Owner's Group. They truly are a helpful and reasonable bunch of folks, and the technical assistance is wonderful.