Collaboration using web server for many pdfs

I manage an online repository of pdfs for multiple clients.  Clients can log in and search all their pdfs by keyword to find what they are looking for and view it in their web browser. 
They want me to take this service to the next level by allowing them to comment, highlight, add textbox etc. and save the file back to the web server doing all of this via the web browser.  They also want to locate their comments that they posted (obviously) at a later date.
A big issue is that these clients have 100s of pdfs that are huge files, some containing 300+ pages.  I researched all collaboration choices for acrobat and I think a SOAP repository would work best for my situation.
Before I start a major project, I was wondering if any of you have experience with collaboration on a remote web server (godaddy) for a job of this size. 
Does anyone think that a SOAP repository is the best choice?  I am looking for guidance mainly as I have no experience developing in acrobat. 
Can I write a program that will allow my goals to be met and work with all pdfs that are ftped to my web server?  I have thousands of pdfs that I manage at the current time.
Thanks for your help!

What you're talking about is called Browser Based Review and was supported up to Acrobat 8.  In Acrobat 9 this was replaced with the newer and more feature-packed Shared Review functionality.
Check out this Adobe TV video:
http://tv.adobe.com/watch/acrobat-tips-and-tricks/collaboration-using-shared-reviews-via-a crobatcom/

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