Hi,
I have bidden for this project yesterday as well. :)
I can give you a script where you just type the website URL and your ref code, and it will clone the website and put your ref codes on the links automatically. And when they click on any link on the website, they will be sent to the real website with your ref codes. This script will work on all kinds of systems, along with Wordpress websites.
I've already done this exact same job on Freelancer like a week or two ago. You can check my profile and look for the job with the "Webpage Recreation Script" title.
If you send me a PM we can talk about the details.