Well, I think driveline angle is obviously the problem!

First, the crankshaft centerline is WAY too high to the pumpshaft centerline (You want about a 2* deflection). AND it is not anywhere near centered left/right port/starboard.
The second is not a huge issue, deflection there ALSO helps cycle the bearings in the u-joints, and that is the reason for the deflection. You have good U-Joints, with zerks.
Doesn't look to me that the motor mount "feet" attached to the stringers were disturbed, hard to say in the pics, are the holes excessively oblonged, or WERE they removed at any time?
Also looks a little "tight" to the pump, but if the thrust bearing is OK with it, then so am I.
Just a thought, but might want to break out a torque wrench and make sure the intake is solid to the hull and the pump is solid to the intake, just to take that out of the equation. I don't think that's it, but best to check anyway.
Edit: What is this chinga-dera jammed in the motor mount?