It seems I have found and corrected the issue. Checking all suspension components everything looked good. Sway links are good, control arm bushings are good, ball joints are good, strut pinch bolts are tight.
I thought to myself, ok, everything looks good, lets double check the top and see that it's still all tight. Checked the three nuts on the top of the strut tower, those were all good. Put a wrench on the passenger side strut nut (the one that holds the top hat and everything together) and I was able to tighten it up a good bit. Test drove and no further noises heard (other than the traditional rear creek from the parking brake cables).
I know other guys have had the same concern, check that nut and make sure its very tight. I was able to get about a 1/4 turn out of the drivers side and a 1/2 turn out of the passenger side. No more rattles/clicks over bumps and uneven roads.