I tried Elastix and did eventually get it up and running, but I found it to be very hard to use, extremely slow, and I wasn’t impressed with the results. So ultimately I abandoned it in favor of Photoshop’s Edit -> Auto Align Layers. Now I ended up writing a script to manage the process, but I bet if you stored two image sequences in a folder, e.g. version_a_001.tif, version_b_001.tif and you record a new action that opens both files, locks one layer, selects both layers, does an Auto align Layers, saves the result as aligned_001.tif and closes all open files [stop recording] you could then simply run that action as a batch command and it would process the whole folder.
Another thing to try is to layer the two versions of a shot in After Effects, apply your LUT to match the colors and then set the blend mode of the top layer to ‘difference’. When everything is the same color and perfectly aligned the frame will turn black. It’s hard to match the colors perfectly, even with Dre’s tool, so that’s pretty rare, but it will be still be easy to see when the frames are aligned correctly. Manually nudge the top frame up, down, left right, and transform the height, width and rotation if necessary until they line up as well as you can get them. Make a note of the transform data, or save it as an Animation Preset. If you’re lucky, the same transform can be used again on other shots, and if so you can just apply the preset on every clip to match it up. At least making it the same size and shape will be a big help - then all you have to do is nudge it left and right if only the cropping is different.
Here are a couple of videos I created which demonstrate these techniques: