I had the same issue with my truck. 01 w/4.6L. Changed the thermostat twice, flushed it twice, no help. Bought one of those small thermometers to stick in the vents, air would only come out at aroun 80-85 degrees. Took it to the dealership, they found the heater core mostly clogged. 1100 bucks later at my Ford dealer, now the heat comes out the vents at around 150-160 degrees.
I have also heard that it could be the blend door in the heater box. Either way, it requires removing the dash to change that too...