If the files are numbered sequentially, you can simply bring them in to After Effects as an image sequence, AE will consider the set of images video footage.
Tracking: You can track two of the peg holes and apply stabilization for position and rotation. It is very automated and fast, the main trick being getting a good tracking result.
Cloning: This depends on what you want to clone out. If it is always in the same spot, it is very straightforward, essentially the same as in Photoshop, except that it will do the same cloning for all frames. It the parts you want to clone out are moving around, it will be somewhat more complex.