If you haven't change any motor/trans mounts that could be a reason, especially if you said it was a small vibration. Since your running with only the rear, have you checked the rear rubber coupling?

 

There's only a very small vibration when the front shaft is out. Rear rubber coupling looks ok. My rover guy thinks transmission output shaft, I'm not so sure.

 

It could very well be, but if you have such a minor vibration, I would think its the trans/motor mounts. Imagine how fast the drivetrain is spinning at 30mph. Its worth a try since they are only 25$ a piece I think, and is much easier than pulling the t-case to just check the shaft, when you'll actually have to pull them anyways!