Somtehing could had happend during the first 2500mi? I think Yamaha are solid rock engines, hard to belive it was a build issue! (it could happend but hard to belive!), why was sold after 2500mi? and it had the noice since he got it? of course having metal like shown in the picture is recent, but damage was done before!!.
Great outside looking replacement engine, inner components?
I work in GM and did engine calibration for the 2.8 v-6 engines (did transition from Carb to MPFI) and most engine hadware was the same, except for sensor and actuators, but base engine same, I will assume that in the Yamaha engine could be similar, will be good to see how the story will end up. Great job, it will be very fun to do it.
Tabaso you will revive that bike!, looking forward for a great ending job!