99 Avalon timing isssues

I have a 99 avalon, toyota replaced a leaky waterpump and did a new timing belt around 58k miles. The car now has roughly 60 k and I have had an extreemly rough idle since a few weeks after the toyota service. Toyota said nothing was wrong when I asked about the idle so I took it to a conrads goodyear, where they found that among several loose and missing bolts on the tming cover they chiped the crank pulley and positioned the cams off by 2 teeth on the rear bank and 1 tooth off in front. Conrads corrected the problems and the car ran fine for a few days but now it runs just the same as it did before. The car was returned to goodyear to find that it is timed wrong again, they reset it and said they need to research it some more to figure out what is going on. Any ideas what could cause this? Could the improper timing have damaged the valvetrain?