As I said, I just eyeball the position of the fenders over the tires. I need to make the gap between the front of the front tire to be equal to the gap between the rear of the rear tire. A person could measure if they want, but the naked eye works just fine.
I have a jacks on both ends of the fenders. I just raise or lower the jacks to make the front and rear of the fenders match. 4" of height between the bottom of the fender and the top of the tire is plenty. If one wants it higher that is fine too. I usually stick my fist under the fender and that is the height I make the fenders.
Please remember that i still have the rear axle clamped up. I the front axle and tire to take all my measurements from.
Once you get the fender were you want it, make sure it not tipped. You can now weld it to the frame.