More chain stretch due to higher valve spring pressure is certainly possible; what's confusing to me is the behavior of the left cam, which advanced a few degrees at higher engine speeds when I tested the other SOHC in 2006, and now appears to be retarding, like the right cam. I don't think I can chalk that behavior up to valve spring pressure.
On the gears, I'll bet your diesel gears aren't straight cut. Straight cut gears like the ones in the pictures earlier in the thread are really noisy, but stronger than angle cut gears.