How to properly stitch together many nearly identical photos into a slide show.

I'm not too sure if Final Cut Pro has what I need to complete the following question, but I'd like to ask the group any way. If not, then maybe you can steer me into the right direction.
I just started taking dozens of weekly photos of the same exact view from one location in our town. My final goal is to eventually put one shot from each of my weekly shoots into a time-lapse slide show/video. I have a dominant landmark in each of the photos, and that landmark is "almost" in the same identical location within each of my photos. However, it's not perfect enough. I'd like to edit each photo so that the landmarks within each photo are located as close to the same location within each photo. This will make for a much smoother slide show in the end.
I do have Final Cut Pro, Aperture, and iPhoto. I have iPhoto pretty much mastered, but have yet to put much time into FCP and Aperture. iPhoto offers no type of grid to use as far as cropping photos. Straightening yes...but for cropping...no.
Would anyone happen to know how I can create this slide show with the best results?
Again, each photo taken is being taken of the same landscape from the same location. However, I'd like to be able to stitch (possibly a hundred, or more) photos together to make as smooth a slide show as possible.
Thanks in advance, Gramps.

What version of iPhoto?
Are you running a Managed or a Referenced Library?
A Managed Library, is the default setting, and iPhoto copies files into the iPhoto Library when Importing. The files are then stored in the Library package
A Referenced Library is when iPhoto is NOT copying the files into the iPhoto Library when importing because you made a change at iPhoto -> Preferences -> Advanced. (You unchecked the option to copy files into the Library on import) The files are then stored where ever you put them and not in the Library package. In this scenario you are responsible for the File Management.

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How to properly stitch together many nearly identical photos into a slide show.

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