I would suggest the following to align.
Loosen the steering box bolts.
Loosen the clamp.
Slip the hole cover on and see how it looks. I find it generally helps on these trucks to get everything started before you tighten anything down.
Front motor mounts are a known measurement, by that I mean they were not factory shimmed at that location. On the rear mounts they were, I have seen shims on the frame side as well as the body side. I have never seen more than two at any of these locations (about 1/8") is what that would be. This picture shows the shims.
http://www.flickr.com/photos/advance-design_parts_co/8129510232/in/set-72157631868452754
