It sounds as if you have taken care of your tires. ie rotate and balnce. The steering shock is not a bad ideal to check. This can be done by diconnecting one end and pulling and pushing through its full travel. Should be steady resistance felt over the entire travel. As you indicate that it can be felt both in seats and wheel I dont believe this to be your problem. I suggest that you install the hard top and drive car for comparision purposes. The vibration will most likely be less dramatic. Then I would check the angles of the driveshaft and correct them to spec. Also at this time the u-joint in the driveshaft should be inspected for binding. I suspect that the trans. mount has collapsed causing a change in the driveshfat angle. These diag. procdures are very time consuming and require some very specialized tools. Most dealers do have this equipment.
Good Luck