I know you stated that the drive shaft is a newly built shaft, but I would have it rechecked. I had the very same problem you seem to be having. I checked every thing like you are doing. Was about to give up and decided to to take the drive shaft in and have it rechecked by a different drive line shop and that was the problem out of balance drive shaft also the guy at the driveline shop told me that the cups on some of the imported u-joints are not 100% true resulting in vibration too.
