Hi 2toyotas,
I've a J120 3.0 D4D 2005 as well, mine is an SWB, and when I'm in 3rd gear below 1500rpm I am getting a massive vibration from the drive train. The engine seems fine but it sounds like the drive shaft is going to come up through the floor. This is similar to your observation I think and I too would like to know if it is a normal occurrence with this model. I would have thought a 6 speed would be able to chug along in 3rd at 1100rpm comfortably. My gear box is very grindy too, I'm being careful with it but I don't think the previous owner was.