A couple of things to consider:
1. You may have an air pocket and need to bleed the system. I had the same symptoms, hot on the bottom and cooler on the top. I suspected I had an air pocket and just ran the engine with the radiator cap off (hot enough to open the thermostat but not overheat) . I also bled the system through the radiator petcock.
2. Some people have drilled a small hole in the thermostat to allow a "bleed" through and apparently enhance its ability to open. That also has worked for me.
I'm sure others have lots of experience with this and can offer better advice.
don
