If the fenders line up well now, then pay attention to and record the exact number and location of the "fender" (no pun intended) washers between the fender and the mounting points now. If you put the exact same ones back in the exact same places it should line up almost exactly like it is now.
If you loose track it becomes a trial and error issue and can be quite a nightmare. You need to read a "how to" article to see how adding or taking away fender washers in certain locations changes the adjustment on the fender. That way if you are to wide or to narrow in certain areas you will know which mounting bolts need fender washers added to or taken away from to make the right adjustments. Also fender washers come in several different thicknesses variying by fractions of an inch.
Hope that helps.