I've done several walls this way, boulders and other types of stone. The best way I've found is to find the high point, like you said. Considering the length of the wall, you'll probably want to find a couple of high points (a little variation in hight over that kind of distance shouldn't matter). Say you find a point every 30 or 40 ft. Make sure that point is not too far out of wack with the rest of the span (if it is, maybe replace a stone or two to bring it down). Use a medium to stiff mortar mix and set that piece of cap. Then move out from there setting each stone to that level. I wouldn't bother shimming, because you'll end up having to lift each stone to get the mud under there, making it a wasted step. You could shim and then tuck point mud in from the sides, But I think a bed of mud and a rubber mallet are faster and less aggravating.
As far as adhesion, I would go with a spec mix or any pre-mixed type M or S mortar mix. Considering the length of the wall, you might do better cost wise to mix it yourself (bags of type M and course wash sand at a 1 to 3.5 ratio). Depends if you're comfortable with your crew getting it consistently right.
A couple other things I've learned the hard way:
-Go back along the underside of the cap and shim in little stones to avoid huge spots where the mortar is really visible.
-The joints between the stones on the topside of the cap make the difference between a cap and a very well done cap. go back over them with a sponge after they dry a little and make sure you get all the mortar off the stone.
-Depending on the material, try to rock face the cut edges with a chisel before you set the caps. Most of the stuff I do is Bluestone, and this works well. A grinder wheel works on softer stone, and there's a way to thermalize it with a torch, but it's really hard to explain.
Sorry about the rambling message, but I hope a least some of this helps. Post a pic and let me know how it goes.