We've designed our own radio transciever with an SI4461 FSK transciever IC for two way communication. We use an NV08C-CSM GPS module and full custom on-board computer.
Althoug we lost contact with the balloon on our last flight, it wasn't the fault of the radio module. Since then we have fixed the issues and according to our test we finally have a reliable tracking system.
For a backup tracker module we use TK102B GPS-GSM tracker. Last time it saved our payload when we lost active radio contact with the balloon. I think it is very important to have a backup tracker, it could save your expensive payload (cameras, special sensors) if anything goes wrong.
We have several ground station solutions too. The primary GND is a rotary dish antenna with automatic rotation control, but we also have other smaller stations and handheld devices for backup.
An other important thing is testing. If you develop your own tracker the most crucial step is to test your device properly. Do long range radio tests, GPS simulations and emulations (if available), do field tests, take the payload to a trip on the surface or with plane, etc.