Are you saying that with a dial indicator on driveshaft you're getting 0.014" runout at the back, 0.014" at the center, but able to drive it off scale, exceeding 0.040" at the transmission end? If my understanding is right, and if you have your u-joints properly seated in the rear yoke it sounds to me like you may have a bad pinion bearing, and at the front end maybe a bad output shaft bearing. That said, you may have a driveshaft that's bent or has a yoke installed funky. Have you had your driveshaft checked at a good shop, like Inland Empire if you have one near by? If not look for the place that services big trucks and they generally do car & jeep shafts, too.