First, I would decide what your final movie is going to be. The most universal format right now is HD. It looks like you sized your images to 4K. If you want to stick with that then just make sure your system can handle 4K.
I would use premiere Pro for the initial editing. Just import each days footage as an image sequence. This will make each days time lapse a separate movie. If your system can handle 4K then you can just drag the footage from each day into a P Pro sequence and play them back in real time. You can do all your editing and even warp stabilizing in Premier.
This will be much faster than working in after effects, totally eliminate the hassle of working with thousands of individual images, and save you a lot of headache. When you have the movie edited, if there are any parts that need "effects" or other special processing you can work on those sections in AE.
Thank you for the great advice. That was the kind of expertise I was looking for. I have purchased the Premier Pro subscription and am playing with it. I have managed to import two days worth of stills as "image sequences" and succeeded in adding them to the Video 1 timeline. It was very convenient. I have also played with exporting a few samples to video. Unfortunately I have made just about every amateur mistake in the book during the picture taking steps of my first time lapse project.
If I have days that were shot at different intervals (15 min, 5 min and 2 min), and lets say I want to have a speed of roughly 1 hour of recorded time for ever 1 second of video, am I fixed to one frame rate for the entire export via the built in frames per second (10, 15, 29.97 etc) settings in the export dialogue or can I manually vary the frame rates for individual videos in my timeline?
You can vary the interpretation of image sequences in both AE and Premiere.
You may also want to research third party products that are designed to help color balance and compensate for exposure variations in timelapse sequences. The are largely automatic and can save you days of tedium.