How to codesign automatically generated iOS apps?

Greetings,

I'm in the progress of writing a web server script that lets you create custom iOS apps (basically exchanging logos and a few other things). The web server customizes a previously uploaded "shell" .ipa and re-zips the whole container to send it to the user's browser. That is: we customize a previously uploaded .ipa on the web server and let the user download it for submission to the App Store.

The next step would be to re-codesign the whole .ipa - because we changed the .IPA contents and the user must use his own signing identity - so that he can actually upload it to the App Store.

From what I understand, there is a "CodeResources" file which contains some kind of hash for each resource file in the bundle, and the executable contains some kind of embedded signature as well. To generate these, you'd have to use the "codesign" utility on the user's computer, then use Application Loader to submit it to the App Store. Correct so far?

What I'm trying to find out is:

1. Is there a way to codesign the .ipa on the server (with having the user upload his certificate beforehand), so that he does not have any extra work to do?
2. If 1) is not possible, is there some kind of tool that allows to re-codesign the .ipa without much hassle? Xcode seems to require some project setup work to do just a bit of code signing - if possible at all.
3. Are there any alternative ways to codesign the .ipa files for the user - possibly without having to manually do it by hand?

Thanks in advance!