The way the air works, from what I understand, is that the flow over the top creates a circular bubble in the bed... and that hard bubble (think, rolled haystack) then acts as another piece of body for the new air to glide over and on down to the top of the tailgate.
Of course that happens around 50mph and higher. Slower speeds cant generate that kind of air flow.
My figuring and theory is that the haystack of air, was affecting the bed in some way.
Now that the cover's there, that variable of the haystack has been eliminated to a large degree.
When I left this morning, the truck was cold and hadn't been used in several days. The vibration was significantly worse than normal for the first few minutes of travel. It eventually settled down as the tires warmed up. My issue is not going to be related to airflow.
As far as the alignment goes, my main dealership does alignment checks on every single car that rolls in. They have 2 drop off lanes and at the end of both lanes they have a hunter machine to do a check of alignment on the way in. Probably makes them a lot of money, but the alignment on my truck is good.