The clunk may not be the tranny at all. Excessive ring and pinion clearance in the differential will produce a clunk. You should be starting in second, and there can be a delayed upshift until your car warms up. Did I understand you to sat the trans was rebuilt as well as the driveshaft. Whew!! I would go back and have them check the rear end for excessive clearance..

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Jeff Lawrence
1989 300e
2000 Dodge Grand Caravan SE
No matter what you fix, there will always be something else to fix..
"Warranty" is just another way of postponing the inevitable.