I still have a 360 and have owned several 380's. Raced them all in the Best in the Desert and Whiplash series when we lived in Flagstaff. So, a couple of thoughts:
The 360 is good on gas, the 380 is a guzzler. I can run 65-80 miles at race speed with a 4 gal IMS tank depending on the terrain. The best I achieved with any of the 380's is 65 miles.
Suspension: either bike can be revalved for you needs, not much of a concern or too expensive. However the 98 380 shock was the worst of the bunch, the 2000 was good, as were the 96 and 97 (Ohlins)
Handling: the 2000 is better, but both 96 and 2000 are good.
Both bikes are fast. How fast do you want to go? the 380 will get you closer to 100 mph than the 360.
$2500 for a 360 is the high end assuming it has all of the goodies
$2800 for a 98 380 is high as well.
I think we are getting into the difference between the Arizona and Texas markets.
In the end, you are purchasing a used bike. Maintenance is more important than year and price. A poorly maintained 99 is worth less than a 97 that has had good care in my book. Look at the wear levels of the pads and rotors, tires, chain and sprockets, ask when the clutch, top and bottom ends were replaced last and base your price accordingly.