Based on the failed bushings measurements I would say that was pretty likely to be the issue.
Putting grease on the input shaft is supposed to be a no-no because it can get on the clutch. The thing I've screwed up before though is installing the input shaft dry is not the same as installing the bushing dry. The FSM says the bushing should be soaked in oil, and to use a teaspoon of grease in the cavity behind the bushing. The input shaft itself should not be greased.
And the bushing should not be magnetic. If it is, I’d get a different one.