I sold a very clean 1998 FE recently for $5200.
I don't think $4500 is crazy if it were pristine, but it should also be running perfectly, and have an after market exhaust to boot. 'Rough idle'.....man, that could go anywhere. Getting a good Duc shop to look at it would be wise. Keep in mind that a 'smooth' idle when an old Ducati is cold is a relative term......
Make sure the headlight isn't cracked. Those puppies are pretty $$$ to replace IF you can find one.