Hi, I'm Matt and would like to help you (23 years an IT developer, webmaster and multimedia pro).
So you would like to have animated videos about your website portal with symbolic (not actual) objects instead of menus, images etc? While I don't use After Effects there are two possibilities using my skills:
1. Script all in PowerPoint animations and export it to video. The benefit is quite easy changes and if all timings and transitions are set more or less re-exporting again (or screencasting again) is needed for the new video(s).
2. Script it as web page animations using HTML5, SVG, CSS3 and javascript animation library (GreenSock). Here the benefit would be reusing parts of animations for the web page though changes would be little harder.
Either way the deliverables are screencasted/exported videos plus all the source files to edit and recreate the animations (and instructions to create videos).
I would like to see your website first (please send me a private message) and know your video list to see if I can create all.
Looking forward to your reply,
Matt
P.S. I have experience for example to create "fake" website from PSD design, then animate actions and form filling and finally screencasting all to video.
Can you provide the URL of your website?