We also struggled with this when we built our last mobile app, Kindred Photobooks. The best way we found is to basically bundle that information in the link and use fingerprinting to make that data available after install, which is working really well.
You can try to build fingerprinting in in house. Basically the steps would be the following:
1. When a link gets created, appending parameters to the link, or create a link reference in some backend database if you want shortened links
2. When a user clicks on that link, collect a fingerprint of their device from everything you can read in the browser (for example: IP, OS, screen size, etc) and redirect that user to the app store.
3. When the app opens, create a similar fingerprint from the same parameters collected in app, and match it up in your database to the outstanding fingerprint.
4. If there is a match, you can return those link parameters to the app through install.
Alternatively, if you don’t want to build all that infrastructure and handle the many edge cases, we bundled it up into a free service called Branch. Check it out at http://branch.io