Today I composited the 2D animation (the frames from Photoshop) on top of the 3D animation (a batch render from Maya) in After Effects.
Eyes animation
Tongue animation
Final composite
I feel this animation has gone well and I'm pleased with the final product. I took a gamble with combining 2D and 3D animation but I think that it's worked well. I may develop this technique of combining forms of animation for my third year film but that is a task for the summer period.