I think you made the right choice. Probably not IMS although you should get that upgraded to the LN engineering retrofit as soon as you can.
I would have used the rough idle and engine sounds to bargain the price way down, and then taken it to an independent mechanic. A few hundred dollars in labor to determine the faulty part or sensor, and a few hundred dollars max in parts. Hopefully you were able to negotiate down several thousand. Almost anything causing rough idle is easily fixable
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