Haha thankyou very much! Well its all about knowing the core principals, luckily Blender makes almost everything super convenient compared to other 3D packages.
Tracking
Ooo I forgot to mention I tracked it in Syntheyes, but from my limited experience Blender’s tracker is more than sufficient for this sorta thing. This shot was a nightmare as I hadn’t put down any markers at all, I didn’t even intend to use it but the footage from the shoot was cloudy so I had to dive into something filmed a month before!
Markers always help, and you can export their individual 2D tracks to use in the clean-up process in After Effects (I guess you could do the same thing in Blender with little grass textured planes and faded radial transparency maps!). My method of tracking is to not panic, and just go through slowly one track at a time. Eventually you’ll zoom out and have a load of good tracks.
I shoot my footage with a 180-degree shutter speed. Don’t worry if you don’t know what that means, but basically its a lot of natural motion blur (Which I love, especially when there’s gonna be CG!). This makes tracking harder, but as long as you make sure the tracker’s point is in the middle of the blur streaks you’ll be fine! I also like to render with Cycles motion blur turned on as it feels way more natural than the unreliable 2D vector blurs. You don’t have to do it this arguably long-winded way, but I love the extra realism 
In terms of getting ‘good’ tracks, I often find myself stopping and adjusting the tracker’s size/rotation e.t.c. If you do that every 10-15 frames you can be safe in the knowledge that you are pushing the software’s tracking skills to the limit!
Shadows
If your lighting is right, you shouldn’t need to do anything with the shadow renders other than multiply them back onto the footage 
I always create a ground plane, and texture it to roughly match the real ground. Often this just means camera projecting (Blender Guru’s tutorial explains that well enough), and maybe cleaning up parts to get rid of actor’s feet/black boundaries caused by undistortion e.t.c.
I then use a sun lamp and environment map to match the scene’s lighting. I often adjust the environment to match the shadows, then turn the sun on and adjust that. Don’t be afraid to play with the colours/contrast but always start simple!
After I’m happy that my lighting is correct (I often use a mirror ball & grey ball for reference, you can see a bit of that right at the end of the video) I play with the material properties of the ground geometry. This allows me to get reflections in puddles, bumpy shadows e.t.c
If you do all that you should get a pretty close result. Then its just a matter of using layers, passes and division compositing to get a shadow pass against white!
The image above is the final result which I use for the shot compositing. Its just the ground’s layer rendered (so you get shadows but no ship) which is then ColourMix>Divided by the ground’s layer with the ship’s layer ‘excluded’ (Ground with no sign of the ship!).
Mathematically, you only get the pixels that were contributed by the ship! (You can take this further with 32-bit linear compositing and get the illumination in the same pass! But I use this for almost all cases)
You should also see that the shadows look like they are cast onto grass. That’s just a fur system attached to the ground! (Which you can assign as a mask layer for the ship so the grass cuts away at it’s edges!)
Rotoscoping
Your last two questions actually have the same answer
The actors were roto-scoped/masked/cut out for every frame they appeared. This meant I could copy the footage below them and change its colours! Luckily After effects has a load of tools to aid the process, including an automated one that can be coaxed into giving good results. If you look around the edge of the actor’s hoodie you can see weird colours bleeding through from the altered footage below. I could have painted them out but it wouldn’t have been worthwhile. This part took most of my time (bar the ship asset of course).
I hope this makes any sense! And thank-you for your kind words. When I have some time I’ll do some tutorials 