CrazyHorse81,
Assuming that "Pump 1 & Motor 1" is functionally identical to "Pump 2 & Motor 2," I would look carefully at the suction and discharge piping arrangements. The most likely problem is something effectively throttling the flow of Pump 2.
If Pump 2 is not making nasty cavitation noises, the problem is likely to be in the discharge piping. I'm thinking mainly in terms of some item of construction debris being in a position in the piping to restrict the flow from Pump 2. It could be anything: a wrench, wrench socket, nut, smaller pipe coupling, or who-knows-what. Don't overlook the possibility of a check valve that may not be opening fully.
You may be able to find likely locations for a blockage by using a mechanic's stethoscope to listen for excessive flow noise caused by the high local velocity at the flow restriction. If you want to spend much more money on the test equipment, I'm sure that you can find fancy electronic noise sensors or ultrasound sensors, but I freely admmit to being very old-fashioned and a bit cheap.
If the configuration of the discharge piping for Pump 2 is very different from that of Pump 1, that could explain the problem.
Usually, or at least very commonly, pump problems arise from piping or control valve problems rather than from the pump or motor themselves.
As is usually the case, Artisi, electricpete, and the other discussion participants have all provided excellent advice. My experience indicates that an induction motor always do all that it can to put out whatever magnitude of torque that may be demanded by the pump without regard to its own health and well-being without protective devices to protect it from itself. If you actually have a 3 hp motor installed with 5 hp protection, it will thoroughly cook itself trying to put out much more than 3 hp. Since you have not mentioned smelling thoroughtly cooked insulation or other nasty issues, I doubt that either motor is being seriously overloaded.