Eye to eye the YFZ shock is actually a bit longer (just shy of 1/2 inch by my measurements) than the 660 OEM shock (without weight), at least the 06 and earlier shocks. Don't know about the hi/lo speed compression shocks. So I guess I don't see where you're losing travel.
Well I stand corrected. I just went out and measured my stock 660 and my stock 06 yfz shocks and you are correct. I get the same measurement on both 15 1/2 inches. Guess I was going off what people have said about the yfz shocks lowering the raptor an inch and the shocks from my standard travel +2 a arms which measure 16 1/4, but after further inspection have the same amount of rod showing, roughly 5 inches , which is the same as the stock shocks so this should give the same amount of travel, I did not check the collapsed length, maybe some other time.
Man I hate it when I'm wrong I usally research better than this, before I post. I dont like putting out wrong information.