You should find a really smooth surface and drive over that. Sometimes I think I feel vibrations when I drive over imperfect roads but it usually goes away.
Can you provide any info on the trans rebuild? The people that rebuilt mine failed to fix the AWD and your clunking sound could be related. It could also be a lot of other things. Sometimes I get a clunk when I press the brakes. Sometimes I don't.
Are these symptoms found in corners or just straight lines?