Yep, gen1 is 99 to 07, Gen2 is 08 to 11. The oil pans are different on the two. The header tubes themselves bolt into the head, but the clearance of the oil pan is different. Also the midpipe(between header and muffler) is different. I don't think it's any major modification, because several folks have switched exhausts back and forth. If you have the exhaust already or get it fairly cheap it's worth doing, if not, there are plenty of good gen1 exhausts at good prices. There are several in the classified section here.
If you do decide to convert the gen2 to the gen1, comment on your question again later tonight. That way if you haven't received an answer yet, it will be back in the new posts and have more eyes on it. Someone will surely give you the exact details and a how to. I cannot tell you for sure myself.
This a great place to be, everything you ever wanted to know is here, some things just might take a while.