I'm wondering if the mts had a slightly different thickness & changed the ujoint angles a bit or if they are just stiffer. the noise got worse with the gear change so that would point me there but what confuses things a bit is the shaft balancing helped. I would check the angles & confirm that the front yoke moves smoothly by hand back & forth in both planes & the rear ujoint is smooth in its one plane. too many changes at the same time does complicate diagnosing. Keep us updated on any info (we'll get it)