Dan here from the Guru team! Thanks for reaching out today through our forums. :) This is a great question. I did find a couple of links you can take a look at that covers the Ebay Affiliates (Formerly Pepperjam) tracking code implementation for Shopify. https://github.com/gjhead/shopify_ebay_affiliate_tracking and also this link here https://gist.github.com/gjhead/cac8dbac3f22bc45fa26 that shows the coding you can check out.
I hope this helps, and thanks again for posting. :) Please feel free to contact us anytime if you have any other questions or concerns.
Dan | Shopify Guru
We've done a number of Pepperjam integrations for clients (Pepperjam now refer Shopify users to us for installs).
The coding is easy enough (see the links above), jumping through the hoops for their signoff testing is a bit of a mission.
We are available if you want to outsource it.