I've started typing a reply to this thread 4 or 5 times. I keep deleting it and thinking about what I'd do. I've came to the conclusion there isn't a pat answer based on what we know at this point.
A great deal of what a given tractor is worth depends one WHAT brand and/or model we're dealing with. Also, you have to take into consideration the particular area where you're located. Some brands sell better in one locale than in another. $1000 is $1000. That's a sizable "savings". But has the tractor depreciated $1000? More than that? What's a used "BrandX" sell for? Would 11 hours use cause the same drop in value as say, 200 hours?
Long and short, even with the new warranty, could you take this tractor home, put an add in the newspaper, and SELL it for the price the dealer is now asking?
I'd venture a guess that if he offered it to you right off the bat for $1000 "under retail", he would sell it for less. It's not at all out of the ordinary for a NEW tractor to be discounted $1000. Again, that'll depend on the brand (and the dealers margin)
Me personally? If I was offered $1000 off, I'd push for MORE than that. I would try to find "blue book value" of that tractor as USED (albiet in exceptionally good condition and low houred for used) and go from there.