I really doubt that the missing bolt wound up in the transmission. Even if it did, it wouldn't be able to get to where the gears are because there's a ball bearing in the way. I'm going to guess that it's inside the ball cover that's still on the driveshaft torque tube. Yes, you'll need to pull the crossmember out in order to drop the torque tube enough to slide the u-joint off. The u-joint yoke should slide back more than 1/2 inch but unless you move the ball cover back (loosen the packing nut on the back of it and probably clean the gunk off the torque tube to allow that.) I'll bet the inside of the ball cover is torn up a bit if the bolt wedged between it and the u-joint, even temporarily.
Do be careful to put a jack under the torque tube as it will be forced down by the weight on the axle tube if you have jack stands there. It can cause some damage if you don't control it with either a jack or something to hold it in place. You don't want it hitting you in the head.
