Here are a few suggestions from someone that's done a bunch of timelapse:
First, and it may be too late, make sure that your cameras are set to manual exposure. You cannot achieve good results with auto exposure. For day to night time-lapse you need to manually open up the iris as it gets darker. Really good time-lapse rigs have this capability.
Second, use Photoshop to batch resize and process your images to something close to the size of your final rendered video. The original camera images are far too large even for IMAX unless you're planning to do some pan and scan on the footage in post. When you set up the batch action make sure that you maintain the original order of the shots and don't put anything between the file name and the number but an underscore or a dash. Make sure you have enough leading zeros. IOW it's very bad to go from myfilename_99.jpg to myfilename_100.jpg.
Third, import as an image sequence in AE only if you need to do more processing on the image sequence. If your camera was set to manual exposure and the footage is in good shape, and you've resized the images to your desired output frame size, then you'll save time by bringing the image sequence into PPro or FCP as footage.
Time-lapse is very tricky. I've shot thousands of feet with 16mm and 35mm film cameras and a Tobin controller. I've done a bunch with a Nikon F2 with a 250 exposure back. Most of you have probably never seen one of those so here's a photo:
I've tried with a Canon G3 with limited success because the camera's manual exposure settings didn't hold perfectly. Hopefully this will help you figure out how to complete your project.
My timelapse experience was mostly on 16mm motion picture film. The Bolex was the rig of choice. A solenoid fired the cable release. An adjustable cam on a clock motor pushed a microswitch that energized the solenoid. Sometimes we fired strobes.
There are several dedicated forums and blogs for timelapse.
Here is one: