There is a freeware Java program I'm not sure has been mentioned here before. It is called ImageJ but the version that includes all the plugins installed already is called FIJI. It has some of the most configurable image registration options I've ever seen in a freeware program. I've used it to align images and do a direct chroma copy between the GOUT and SE. It's a bit tricky to get the right settings at first and you'd probably have to read up a bit on what all the settings are.

You can go HERE to get an idea of what is involved in using this method.

The most interesting part about automating film footage alignment using macros is at the bottom.

I also use the MOPS feature extraction plugin to get features from both images and then feed it to the bunwarpj plugin for better alignment.

Unfortunately you have to use the RGB colorspace with this program.

**EDIT:

I found a nice tutorial video HERE that shows and describes all of the advanced functions for the plugin. It even shows how to make landmarks and feed it to the unwarp plugin for greater accuracy.