My car is overheating, the heater doesn't work, and only a half gallon of coolant comes out of 3 gallon cooling system

So, I have a 2000 honda accord sedan with the v6 engine. It was overheating, so I replaced the thermostat. That was a year ago. I noticed that there was some gunk in the tubes but because I'm a n00b I left it and didn't think much of it. It was still overheating in the summer, so I just made do the best I could. Then comes winter, not overheating much (gotta love Montana winters) but alas, the heater doesn't work. The tube going into the heater core is hot and the one coming out is cold. Which doesn't make sense, because it wasn't plugged up anyways and it's not leaking. Anyways, fast forward, I try to empty my cooling system so I can do a complete flush, and only a half a gallon of coolant comes out of the radiator. Only a half a gallon goes back in too. It's supposed to hold 3 gallons. I don't really want to mess around fixing 10 different things, does anyone know what really needs to be fixed or replaced? Once I know I can either fix it or hire someone, but I don't want to do that until I know exactly what the problem is and how I can fix it. Thanks.

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