I had a similiar problem with my daughter's car yesterday (bmw, not a yota, yea, sorry) Anyway, after flushing and filling the cooling system, the upper radiator hose was hot, but no hot air from the heater, and the lower radiator hose was cool.
I scratched my head and figured I bunged something up with the thermostat or water pump, or had an airlock. Hoping it was an airlock, I disconnected the upper radiator hose and filled the radiator from the upper hose, instead filling from the overflow tank like before. Sure enough, problem solved, it was an airlock, and everything is OK now.
If you haven't already, you might want to see if you can get any more coolant in (and air out). Good luck.