I have an 07 Civic, had a cracked block, I was out of state so I put some stop leak in it. It stopped the leak but clogged everything else as well. After putting the stop leak in I lost heat except for in the far vent on the drivers side. The rest of the vents blow cold air, while the one blows warm. I've had the heater core checked, it's working fine. Honda replaced the block, radiator, and thermostat.
Any ideas what it might be?

 

heater core

 

Check that the cooling system is full, radiator should stay full to the top.

You can try disconnecting the heater hoses from the engine then flush the core both ways with a garden hose. This will sometimes clear out blockages from stop-leak.