Hey Josh, sorry for taking to long to respond. I think this was accidentally posted in the app development forum. I still haven't made any updates to the affiliate system. I didn't consider tracking click-through to the links but I think it would be a good idea.
I still haven't decided how any revenue sharing will be handled. It would most likely be a cut of the cut the developers give back to itch.io. Since some developers set the cut to 0 there would be nothing left for the affiliates. I'm wondering if I'll need to publish the developer cuts so affiliates can see what the expected revenue is.
If you have any other ideas feel free to post them