If the motors check out ok as you say, ask around for a recommended surveyor in your area, make sure recommendation comes here or at TheHullTruth.com or marina members, not from any dealer.
Take the surveyor for a ride and explain what you said here, about how it was in the past, and now, and the Yamaha motor report.
If he gives boat structure clean bill of heath, and he will know where to look, then live with it.
If you have no experience nor don't know what abnormal looks like, this isn't the time to learn by yourslef, just hire it out.
Same goes for buying a house, the engineer's report is same as surveyor's report typicaly done by buyer when buying a used boat.
You can be present during survey and ask all the questions you want. Make sure you take surveyor for ride and note the noise when it occurs.
Boat structural failures including rotted stringers, transom, and bulkheads, glass tabbing delamination, can do exactly as you report on any boat brand, including Gradys.
Good luck.