how to align rotating motors to pump shafts?

Answer 1

You can buy one of the tools shown below. The mechanical one features two dial indicators that attach to one of the shafts and extend over the other shaft. One indicator is pointed radially toward the shaft and measures variations in position. The other is pointed toward a vertical surface connected to the "other shaft" and measures angular misalignment. By rotating the shafts a little, you can see how much things are out and shim your motor accordingly.

Answer 2

http://www.tpub.com/fireman/67.htm

This works quite well for the inexperiemced.