I have never used the Windex method, or heard of anyone using it on shroud graphics. I don't reccomend it.
I have Factory Effex OEM graphics on my RM. They are pretty flexible once you start putting them on. While I was putting mine on there was one area that I just knew would not fit correctly...so I got out the razor blade. Well, once I got the whole thing on, I was looking around for that little piece of sticker I had just cut off. So give them a chance, you'll be suprised.
If your graphics had the bolt pattern cut in it, start by lining those up. If not, start lining up the curves at the very front edge of the shroud(for bikes that have a concealed gas tank; KX/CR) or the very back (bikes that have exposed gas tanks; RM/YZ). This will be your reference point. Once you have an idea about what looks best, start peeling off the backing, about 3 or 4 inches at a time beginning at my reference point. Once you have it sticking at your reference point, keep light, constant tension on it as you lay down the graphic. This will prevent kinks and bubbles. Remember, if something doesn't look like it's lining up, the graphic can absorb minor curves and adjustments with out buckling.
Let me know how it goes.
Have patience and fun! Good Luck...