I did read your post. Do the job in Premiere Pro. If you want to you can write yourself a script, come up with a naming structure and a folder structure and have the script automate the assembly of rendered video clips, but you will be doing the job in AE and your renders will take four or five times longer than doing the job in Premiere Pro.
A few weeks ago I took 4 days of filming, about 20 pages of scripts, most scenes had the actors fixed up with wireless mics recording to their own individual tracks so in many of these scenes I had 6 to 8 streams of audio. There were hundreds of shots and about 4 times that many audio files. by importing in the appropriate bins in Premiere Pro, shift selecting the individual scenes and creating a sequence for each scene, then shift selecting the appropriate audio tracks and dragging them into PPro I had the entire 4 days of filming ready to sync the audio and do the first edit in about an hour and a half. I used a 3rd party solution to sync up each of the audio tracks with the video tracks instead of using the slate or messing with timecode. Every scene, every take was ready for review and comments in less than 2 hours.
Give me 100 different intros in a single bin and 100 outros in a second bin all properly named and a common middle section and I would click intro 001 from bin 1, Ctrl/Cmnd the common middle part from it's bin, then Ctrl/Cmnd outro 001 and choose create sequence from selection in about 15 seconds. Yes, this is a bunch of hand work, but so is writing a script.
Once you have your first 100 sequences created in Premiere Pro, providing that your first and last shots don't change, all it would take to change the middle shot in all 100 sequences would be to close Premiere Pro, move your old middle part video from it's current folder to a new one and give it a new name, then put the new middle section in the original middle section folder and make sure that it has the same name, something like Middle_Section.mov, that the first middle section video had and then open up Premiere Pro again. You're done.
I actually have done something very much like this many times in my NLE editing career. I would create something like a show open, then name each new opening title something like Feb01_open.mov, Feb02_open.mov and so on and save them into a folder called Feb Opens. Then I would copy the .mov file to the proper source folder and change the name to open.mov, open up PPro (or AVID or FCP, or even AE) and the new open would be there without any more work than renaming the file.
If you want to dive into Scripting for Premiere Pro check out this thread: SCRIPTING for Premiere Pro |Adobe Community​
Then explore the Scripting community and resources. Once you have the script written you will have to carefully follow a naming and folder structure.
I hope this helps. You will not find a pre-writen script that is this specific, but there is nothing keeping you from spending several days trying to figure out how to do if for yourself.
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