I was going to suggest searching ebay for 'completed' auctions, but I could not find any 2006 GSXR 1000 engines. Maybe I did the search wrong. Hard to believe there would be none. I like to look at the completed auctions because they give a better idea of selling prices. Active auction prices are all over the place.
Here's one:
http://cgi.ebay.com/ebaymotors/GSX-R...item3a5b67e53e
Two thoughts: Is it too late to decide to just run the '06 engine that was in the car? That would save a lot of hassle, and maybe money. I doubt you'd notice much difference in lap times in your first year.
The prep shop that is doing the swap for you - Do you think you could convince them to sell the '06 for you? That might save you a lot of aggravation, too. It might be hard to sell an engine you don't have in your possession and don't know much about.