Both transmissions can be used on a 5,9. It's the bell housing that is different. The AT545 uses the SAE 3 bolt pattern, and the MT643 uses SAE 2. If the MT643 comes with the bell housing, you may be able to use it. Of course, there are bound to be some other differences to sort out -- perhaps the flex plate (fly wheel) I don't know. The MT643 is longer, so the drive shaft will probably have to be shortened. This is no big deal in any sizeable town with a drive line shop. The MT643 is a much better tranny, so you will be better off with it. If the mechanic says that he knows what he is doing with this swap, and the price is fair, I would probably jump for joy. My 40-footer has the 643. Your bus is probably shorter, and thus lighter, and therefore came with the smaller tranny.
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