Just my opinions:
1. Nothing about that PS installation looks factory.
2. That cantilever pump bracket is pretty weird, and could be causing some resonance. I would pull the shaft off and see if the noise is in the PTO or the pump. I set up all of mine for a self-loader from scratch, and it not only was not
that noisy but it looked better too even with all the salvaged and cobbled together parts. If it's not pump noise, then I guess drain some gear oil and pull off the PTO and inspect and turn it by hand.
3. Probably, but I wouldn't trust that tubing to frame weld