I think to have more control and to get more money out of it, you should sell the soft-top separately from the truck. Sell it with the hardtop on, and mention "I also have a brand new soft-top that I'll sell for $xxx" And if they do want both then you can do a package deal...
The soft tops are hard to come by... you can get $400-600 easy. Just selling the hardtop by itself, you'd be really lucky to get $100 (especially since a lot of K5 guys want the sliding windows).
If you were to sell two identical 1009's one with the hard top vs one with the soft top...the difference in price is probably fairly negligible...maybe a couple hundred bucks. Unless you're selling it to a hardcore military vehicle purist.