300 tdi transmission rumble

HI guys. Still chasing a very slight vibration and rumbling noise from under vehicle . It occurs at 55 to 60mph and loudest on inclines. If I dip the clutch its gone. Put transfer box in neutral its gone.
Fitted new tyres recently , and new front prop (slight play)and a rear rubber universal joint old had elongated holes ! and still the same noise. . How does one check if a rear prop shaft has been separated and joined again correctly, are there any alignment marks ? Is it likely a diff bearing or front transfer box output shaft bearing ? Any pointers appreciated thanks.

the 2 innermost yokes one each end should be in the same plane as in pics linked
Google Image Result for http://image.made-in-china.com/2f0j00jCpQnJawyykl/Drive-Shaft-72-2203010-A2-for-Mtz-Tractor.jpg
also you can remove one prop at a time and run in diff lock see if removing one cures rumble

Thanks James, but how do you check alignment of rear one with the rubber joint

Progress.... I removed front prop and rumble is gone ! The front prop is new, so i suspect either front diff or transfer box output bearing, which has a tiny bit of movement up/down , read on threads this is acceptable ? Any advice welcomed . Thanks.