I'm not 100% following your current process, but I can answer your larger question around tracking. There are so many options!
We've set up partner micro-sites where we host content. This sounds similar to your situation - we want to know what content was downloaded and which partner's site they came from. The content piece is easy - you can tell by which form they completed. The partner is just a URL parameter that passes to a hidden field on the lead.
If you can expand upon your process I can answer with more detail. Why does every email send need it's own URL? Do you have a screenshot of your granular report? What data values are changing? Do they change when an email is sent or just when someone responds?
Sorry, I have more questions than answers at the moment.