First:
Manually back flush and top fill the heater core. Pull both lines off the engine side, run a hose through them until water comes out clear in both directions. Then drop one line, blow through it, and then hold them level, stick a funnel in one, and fill with coolant.
Next:
Check that the rad is full with the engine cold. Not frozen, cold. Start the engine with the cap off and the rad full, the fluid level should drop slightly indicating flow. If so go drive it 2.5 to 5 miles. CAREFULLY, like holding it with a rad and be ready to jump back carefully, pop the rad cap off and check the fluid level. Top off, replace cap, go drive 10 miles. Remove cap as before, top off fluid. Repeat. Now you should have all the air bled and burped out of the system.
Your problem really sounds like a low fluid/air pocket issue. It is really hard to put the thermostat in wrong since they only fit one way (yes, I tried).
