Tom S,
Did you replace the rag joint when you replaced your hub and drive shaft? Rag joints stretch and deteriorate over time and if the holes are worn/elongated, that can cause drive shaft to be off center and result in excessive wear on the hub end and premature drive pin failure. Also, are you using an OEM hardend steel solid drive pin? A hardware store roll pin will not hold up to the force of each power stroke from the engine very long.
There's not much adjustment on the engine but you can loosen the four bolts attaching it to the frame and move it slightly if you think the engine is cocked a bit and binding on the shaft but I would first be focused on the rag joint end. My $.02. Hope that helps.