You certainly can try the different fuel source--and that is the cheapest and easiest.
Since you already spent some considerable coin for this motor, I would think that the shop should stand behind it. Hopefully they missed something (or maybe didn't do as good as a job as you paid for?)
Did you personally change the pick up screen, and clean the tank? It could take just one little bit of stuff to cause a problem.
I don't know much about the Vapor Separator/High Pressure fuel pump, in that specific outboard, but if Marc says that could be an issue, he is a man who knows those motors! The injectors and injector pumps have to have clean fuel, or there can be issues. Even if cleaned, and one place was missed, then contaminated fuel got down the line, it could now be a problem.
The fact the boat seemed to run well the first for hours, suggests that something was picked up, and is now down the line in the fuel system.
Since you are not getting enough power to plane, at 3800--this certainly rules out the spun hub. I assume that you did pull the plugs, checked the gap and condition.
Good luck--and keep us all in the loop.