Joe - Where do you have the jack stands/supports set up for the rear of your truck? If the rear of the truck is supported on the frame, with rear axle hanging down, the jack under the front of the torque tube should be able to raise it high enough for the transmission to clear. If the axle is resting on jack stands, it might reduce the range of motion and not allow enough room to pull the transmission.
Did you leave the collar and the ball on the torque tube when you disconnected it and slid it back to access the u-joint? If it's still on the torque tube, you may want to remove it if its not allowing the torque tube to elevate as far as possible.
Pictures would help offer more/better suggestions.
