Andy it sounds like you did the same thing Doug and I did. I came up with a little cleaner method on my YJ ( sorry Doug you were the test Jeep). I cut the metal about 1/2" longer then the opening I wanted. I then took a short pair or channel locks and bent a lip inwards so the lip was about 1/2" wide (hence the 1/2" left when cutting). With several differnt size hammers I tapped (not beat) the bent lip until it was flat. I took my time with the hammer and the bending and from only a few feet away it looks like a factory lip. Since the paint was a little rough after the bending and hammering I hit the lip with a little truck bed liner and put the flair back on.
This method takes a lot longer, but the results are clean and the lip provided a place for the innder fender linder to go into, which isn't on the XJs.