The way my indy does it is by charging a margin over the cost of the used piece. This is sort-of like buying an extended warranty from him...it's not written that way, but he assumes the liability of working with the salvage yard to get the best possible unit from them. He warranties engines and trannies for 10k miles or 6 months, and the markup is not extravagant (like 20%).

If the indy will stand behind both the work and the trans with a guaranty, there's no reason not to save the $$$.

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1973 280 - Current Project Car
1979 240d - 100% Stock
1982 380sl - 100% Stock
1985 190e 2.3 - Heavily Modified