Did moving to Helicon ISAPI Rewrite help anything? I would be surprised if it did. I used to use that, but had to ditch it and now use just the Rewrite module built-in to IIS 7.5. Why do you have to force the content length anyway? That seems like a big potential break point.
Also, I am not aware of a program that will re-write the existing links embedded in your HTML code, if that is what you're asking. Of course if those links are in a content field that you can manipulate with ColdFusion beforehand, then you can customize those links using CF however you want.
P.S. The IIS7 Rewrite module has example templates built-in that should show you how to craft a custom response to any scenario, or at least ge the ideas flowing. They are under the SEO section of the "Add rule" dialog. The "User-friendly" mapping should all give you ideas.