Yes, in fact I did this very same thing. I bought the 2010 boards and gutted the 09 mac pro boards. Yes, they will fit in the same case as the boards are exactly the same. I got mine for 300 last year, but that was the luck of the draw. You would be lucky to find both for under 1000 these days.
The w3680 is around 500 bucks, should you desire 6-core power.
So, yes.. taking out the 09 boards for 2010 boards in an 09 is indeed possible, but at this point, not worth it. In case you want to know. I got my 2010 boards(backplane and single quad board) through a local Apple Service Center and paid the following:
49.00 for the single quad board
250.00 for the Backplane board.
You won't find these at the low prices I once paid.