mixed info on setting pinion angle?

When setting pinion angle should the car be on jack stands under the frame letting the suspension hang or should the car be up on blocks. I have checked my angle with car on blocks under tires and I get tranny down 1.5 degrees and with 2 degree shims the pinion is up 1 degree. This all comes from after doing a auto to 4 speed conversion. After doing conversion I had a thud when starting to back up. One person said needs new leaf springs, did that no help. Another said pinion angle, hense the 2 degree shim. That almost got rid of it but does it still slightly. I have another set of 2 degree shims and was wonder about trying them but then pinion will be up 1.5 degree more than tranny. So what is correct method and thoughts on degree difference.