Importing and Compositing in After Effects
Now that we've got all our render layers we can import them into After Effects(AE) for a composite test. After importing drag your background frame onto the composition icon and AE will create a composition with the right size. Now you can start dragging all your CG layers on top of this. Here are a couple of terms I won't get into in this tutorial which are important to understand to achieve a nice result:
I'll break down how I did this composition. Starting with the main body I added the diffuse layer. Then I added the specular layer and used the 'add' function to make it add the highlight to the diffuse. I made a pre composition of my reflection passes (included the window reflection) which I then added over the diffuse, again, using 'add'. Then I made a pre composition of all the main body parts.
Remember that all of these layers can be adjusted separately for a good result.

Setup for main body. All of the layers have alpha channels so no need for a matte

Use do the same to create a wing composition (I'm sorry but this was rendered at a different frame so the position is a bit off)

Now let's add the wing composition and the main body composition on top of the background image and...tada...we've got something going on!

Shadow and occlusion
The shadow should be fairly simple. Just add it between the background and the main body layer. Notice that it covers up Seans feet as well but we'll deal with that later.

As the occlusion layer affects both the main body and the background using a 'multiply' function we need to remember that this has to be done on top of the main body and the background to have an effect. When pre composing two layers the background information disappears so the blending has to be done to the pre composition itself. To be able to adjust the occlusion on the ground and the main body separately I used the RGB-matte pass to separate the two in a separate composition before multiplying it on top.

Separate the ground and main body occlusion using the RGB pass a sett matte gives greater control
Add the occlusion composition on top and multiply to darken.

Composition with occlusion pass multiplied on top
Ok..now we're getting somewhere..we've got all the layers in there ready and recomposed but....not very realistic....I won't go through all the details on the adjustments but commonly used effects and settings are curves, hue/saturation, matte choker, blur and layer opacity. This all depends on the footage and your eye but with the setup you will be able to have a fairly good control on the different parts so play around with different settings and see what works. You also want to add some noise to the clean CG elements and AE has some tools for calculating and adding noise from the original footage.
At this point you may find that you have to re-render or add a pass to get a nice result. If this is the case go back to your 3D program, make adjustments, re-render the frame and reload or add the footage in AE (note that unless you make big changes you should not have to render all the passes again).

Final frame test after ajustments to the different compositions
When you end up with a frame you and everybody else (other than your mom :) is happy with you can start to render the whole sequence.
When you've got everything it should be pretty easy to add the different layers, redo the effects and settings from the test frame to reproduce it. Of course you'll probably find things that are not working and you may have to render some passes again if it is impossible to fix with corrections in post.
Motion Blur
As I said before I did my render without motion blur because of the render time but it is a definite must to make your CG elements blend in and look realistic. In this case I took a shortcut and added motion blur in AE. While this is less accurate and far from realistic it was my only option. To achieve this I used a 'radial blur' in the wings pre-composition placed in the middle of the wings and hand animated to keep in the right place. The directional blur can be used as a substitute for the blur of the main body but this have to be done carefully because of the minor movement (the length of the motion blur depends on the cameras shutter speed so brighter environment will produce less motion blur).

Final render with added motion blur
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