Chris,
This is an interesting project. I've always wondered how long it would take for someone to make a Muppet Fan Film. Half thought about it myself but I have bigger projects on the forefront for now.
Some thoughts on your greenscreen. Obviously, somebody mentioned Kermit since you used his desk as one of the images. You will have to use another color for the chroma on that matte. Bunsen will probably also be an issue if he is the true chartreuse color of the original Muppet. Chroma (I'm sure know) will be able to pull some of his color if it's close. That why most all shades of the certain color can disappear when you use a chromakey backdrop. If it doesn't then you may still have issues with the outline of his features looking fuzzy (and not in a good way) against the background. Any color can be used to chromakey but green and blue are used primarily because they are farthest away from the color of human skin. You'll have to make adjustments accordingly and make sure you have strong rim lighting so they (the puppets) will show.
I don't want to sound like Debbie Downer but I opened up several of your images in After Effects to look at them. I don't know what resolution you plan to format the final film but at their current size, they look rough. They are pretty pixelated. The edges where you've created your matte really need to be feathered and adjusted to seem less harsh. If you make the final film frames smaller it will be less noticeable but there will be greatly diminished detail and the film quality then suffers. My prediction is if you use them as is, you are really going to have a lot of artifacts and traces of the matte left in the shots which will really make it look noticeable. Matching lighting looks like it may also be difficult.
To recreate these sets as CGI you will not be able to do it in illustrator. You will either have to use Lightwave, 3D Max, Maya, Cinema 4D or some other type of program that let's you create and render objects in three dimensions. The good news if you do it this way it lets you scale, move rotate the sets, camera, and lighting on all the objects you create. Then you can matte out what you need and create this you wouldn't be able to do on a practical set.
Again these are just my thoughts. While I am no expert I am in currently getting my BFA in Computer Animation, specifically, visual effects. Hopefully you will put together a strong team to help you pull it off.
Janice looks great btw!