I wouldn't use any axle with a "wow" in it, regardless of where it was located. That's got to put stress on the bearings, and yes, you will see it at the wheel. If you want to keep from replacing the entire rearend, you might look into a set of aftermarket axle shafts. Check the flaps, you might be able to still get replacement axles for a reasonable price.
On the bumper issue, I would suggest taking the mounting bolts loose from the frame. Just loosen them enough to allow you to "float" the brakets around a bit. That should give you enough slack to alighn the bumper to the brakets. Get the whole thing centered, then tighten the bolts.
