Look very closely at the worn areas. Analysis can tell you a lot. Is it from abrasion (relative sliding motion) or impact? Which areas are worn and which aren't? Why? See any fractures or cracks? A little detective work can tell you a lot.
My gut tells me that you have a problem with shaft flexing and inadequate bearing alignment. Even if the bearings are in absolutely perfect alignment (which is not possible), they still need to tolerate shaft flexure without causing damage. How much is the shaft deflecting? Once it deflects at all under load if the bearings don't flex with it you have a problem.