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You would probably have to make a "brand guide" in XML or I would use a spreadsheet for each client. You need a template for your clients' headers. The template would fill the design elements from XML set Client logos, info and colors, then fill the rest out with the resulting data from the surveys. Report two would repeat. Styling from XML set for Client two, then results. Or the alternative is to make a 1000 templates and drive yourself nuts updating. But the key is to make another XML containing clients' data to fill the header.
Added: You can run it from the web app. When a survey is done, have it automatically spit out an XML into a "watched folder" on your server, and then the script could be activated. Email the result to let someone check it before sending it to the client. This is so if there are any errors you see it before the client gets in an uproar and adjust any scripting or encoding needed, XML is funny with characters other than letters and numbers.
I set up a similar system 3 times over the years using Applescript and PHP with Excel. It's quite intensive and you definitely need to break it up. Most times, we had the previous script calling the next script when the code finished running as a bridge to keep from getting occasional errors from the computer not catching up.
VB Scripting Guide for Adobe InDesign for reference CS5.5
Samples of scripts for Reference