Motion tracking issues

I am doing a rather difficult (for a beginner) sky replacement on a panning shot.
My first issue regards rotation. I've selected position and rotation for my tracking points, but after applying them to my sky layer, it becomes flipped upside down (rotated 190 degrees) and also out of position. Correcting the position is as easy as selecting all the position keyframes and dragging it to the correct starting point, but for rotation this doesn't work (it sets everything to one value). I want the first keyframe to be 0 degrees and for it to follow on from there with the tracking.
Secondly, because the camera pans quite far, I need to change the tracking points midway through as there are no two points I can use that are in the entire shot. Similar to the first problem, I find that when I do this it resets the position of the sky layer, sending it out of place and upside-down. I guess what I'm looking for is a way to apply the motion tracking to the sky layer without losing its initial position or rotation (or any other value for that matter).
Thanks!

Thanks a lot, I do have mocha but have never used it as I'm still in the early learning stage of AE. I'll watch through a couple mocha tutorials though and see where that gets me.
Regarding the matte, I was intending not to use one as there is so much foliage detail it seemed impossible to key the sky out effectively. Instead I was just going to multiply the sky layer and apply a gradient. I've attached screenshots showing the start and end of the shot, before and after I've done my best on it. If you know a better way I can do it, I'd be very grateful.
Cheers.
Source beginning:
Source end:
With sky layer:

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