How would you attempt this composite?

Here's another workflow I have used when the transition between shots is more complicated. 

Here it is in a nutshell.

Pick the part of both shots you will use for the transition and trim them with a few extra frames on both ends. Pre-compose both of the trimmed shots. Apply Mocha AE, then track the background with translation only, making sure you unlink the spline from the layer. When the track is good, lock it, then add another spline that will be used to cut out the transition area, like a tree and everything to the right of it. Link the spline to the background track and make any adjustments you need to so the roto is complete.

Repeat with the second layer. You now have a left side mask and a right side mask on two layers. 

Gather the tracking data from Mocha AE, invert it, and apply Translation only to the same layer. This will stop the camera move. Add a null, parent the motion stabilized layer to the null and move it in the comp frame, so the mask is about halfway through the shot.

Repeat with the second layer. You should have a composite now where the seam between the two shots does not move. 

Add another null and apply the Tracking data from the ending shot to the null, making sure that Invert is turned off.  Parent the null from the first shot to the null from the second shot, then parent the second shot null to the third shot. This will put the camera movement from the first shot back in the first shot and match the second shot to it. You can then adjust the anchor point of the third null to line up the shot, the speed should match, and the invisible joint will be as good as your roto.

I don't have time to knock out a tutorial on the workflow, but those are the basics. I don't know of a tutorial I can point you to that uses this workflow, but it works well, and I have used it about a half dozen times in the last couple of years. 

Let me see if I can describe a workflow that matches what I think is your post-production problem. 

The two shots are as follows. 

Shot 1: A hand-held right to left pan of a forest scene with a bunch of trees that covers an arc of about 60º

Shot 2: A repeat of the hand-held pan in shot 1, covering the same arc, but this time, an actor is walking through the scene

The final shot: A hand-held pan through a forest scene but halfway through the pan an actor magically appears in the scene walking between the trees.

If that is the basic idea, combining two pans of the same scene with a seamless transition between shots, then this would be my workflow. I. threw the actor into the second shot because that would be something that is obviously different between the two shots.

Here's my workflow. 

1. Add Both shots to the timeline, the shot, the one without the actor, on top
2. Move down the timeline to the point where you want to transition to the second shot and set a marker
3. Change the blend mode for the top shot, or add a mask that cuts the shot in half horizontally so you can see the shot on layer 2
4. Slide layer 2 left or right in the timeline so that the two shots line up as close as possible under the marker; You are looking for something like a tree hitting the center of the frame.
5. When you have the first and second shots lined up as close as possible, decide how many frames you want to use for the transition and split the layers (Shift + Ctrl/Cmnd + d) 
6. Disable the mask so you can see the full frame overlap at the marker.
7. Using the difference mode or another blend mode, fine-tune the position of the bottom layer using position, rotation and scale if necessary to get the frames to match up as closely as possible so you can make a seamless cut between shots. There will be a shift in the frame edge when the cut is made, but that will be fixed later. 
8. Preview the cut to make sure that the cut, not the speed, is seamless
9. When the cut is seamless, pre-compose the second shot, trimming the pre-comp to the layer length and moving all attributes to the new composition.
10. Enable Time-remapping on the pre-comp and move down the timeline about a second, and set a second time remapping keyframe. 
11. Drag the top clip's out point to the new keyframe you added to time remapping on the second shot and enable the blend mode or turn on the mask so you can see the timing difference between the shots
12. Drag the second time remapping keyframe left or right until the timing of the shots match up
13. Reset the in point of the top shot  to the marker so there is a seamless cut.
14. You have now matched up the frame where the cut is made and the speed. Pre-compose the two shots and scale up the pre-comp to hide the edges of the frame.

I have used this basic workflow many times when rotoscoping was not an option. 

For your shot, you may have to animate a mask along the right side of the tree and overlap the frames a bit to hide the shift in parallax. It's completely doable. You just need the right mask and the background framing and speed to match up.

That's probhably a case for a full re-compose. the lack of motion control isn't even the problem, the parallax simply appears completely wacky and unbelievable. I'd probably slice & dice the tail end and start of shot A and B, respectivley, and create an artificial inbetween.

Mylenium