Go ahead and weld them. If you use a mig welder and have new angle strips, plug weld them from the outside of the bed. This way you won't have to do any grinding or sanding on the strips themself. You will have to grind a small amount in front and rear of the fenders. Don't worry about what is behind the fenders, you can't see them anyway. With pop rivits. they would show and might not look quit right. It sound like you are doing all the right steps, don't stop now. Also, the angle strips are what hold the bed sides up. Everything starts from them. Pop rivits may work loose.
Make sure you get the angles in the right place and straight. I got mine a little bowed in the middle. No one can see this but me, its just one of them thinks that make you mad. Joe
