Ri217 engine/boat vibration

[Ri217 0]

Bought my ‘17 Ri217 about two years ago with about 327 hours. End of last summer with just over 400 hours, I changed out fuel filter and oil/filter. I believe it was the next time I took it out the boat started having a weird and noticeable shaking/vibration while at surf speed. After an hour or two the boat died. Got towed in. Come to find out the fuel relay blew out. Took it to my boat mechanic and he replaced and plugged it in to his computer. Everything seemed to be fine. Took it out again and boat was running the same and about an hour later it died again. Long story short I took it to a centurion shop and they check the boat out and replaced the harness by wiring in a new fuel relay harness bypass. They ran it and said it was running fine with no vibration. 
So I took it a few days later and right away the vibration was there and when I put into great the vibration was worse. So it’s back at the centurion shop and they can’t seem to figure it out. 
My guess as a non mechanic, after reading a few forums is it could be low fuel pressure from the pump? Transmission? Or she’ drive shaft/ shaft seal? 
Any ideas? 

Thank you!