Be sure to lubricate the nipples with a light lube. Hit both the area where the spoke enters the nipple and where the nipple exits the rim. Problems at the seam are common. When you say "bump" are you saying the rim moves away from the hub, or the rim is moving toward the hub, at that area? If the rim has not had an impact there, you should be able to minimize the problem, but it may never be perfect, yet is it likely to be useable.
See
Wheel Truing
If the clicking if from worn cones, the hub would certainly be worth a rebuild.
The teeth on many modern systems appear to wobble back and forth. This is a design to help shifting. Spin a new cogset if you can find one to compare.