You could probably get ahold of wetsounds and I am sure they could fix you up with the right bolts, or hit up a hardware store or automotive store to find what you need.
As for your issue with the pre-drilled holes, If I were you I would temporarily mount the clamps where you want them and then mark and drill new holes to make it look cleaner and avoid having to run the wires between the clamps and the tower bar. You should be able to find some plastic plugs to fit in the old holes (again, a hardware store should have these).
Here is a picture of mine and as you can see there is some amount of gap between the clamp and the bar, but you run the risk of the wire wearing against the edge of the clamp and I know the diameter of the Axis towers is larger than most so you may not wind up with much gap anyway..
good luck