I have always felt like my body is just a puppet, my skin, my shapes, my movements never felt natural like it is me. I was wonder does this feeling lessen as I continue down this path.

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Yes I believe it will lessen as you transition.  My body feels more real since starting to be me...each step I take brings me one step closer to alignment.   I believe the disassociation you feel is the misalignment between your internal and external identities. 

That feeling has vanished for me and it was not till I accepted myself as transgender and gave up the "man act" that I recognized how much work I was putting in to modifying my behavior. 

I would hope you will continue to feel more authentically yourself with better alignment going forward.  Keep it up!