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When I removed the coolant I saved it to pour back in after changing the thermostat. I still have three quarts left that won't go back into the radiator. Do you guys know why this is?

Did you remove it before doing the heater bypass? If so that would be where it went. If not, possibly there is an airlock preventing the rest from going in. Sometimes if new thermostats are sealing tightly it takes awhile for the air to bleed past. Some get around that by drilling a small hole in the thermostat flange but eventually the air will bleed thru and the level in the radiator will drop so you can pour more in. Also, the remaining heater hoses might be empty. That wouldn't account for more than a pint but you can open that valve and let the hoses fill then shut it again.

Good Evening Brenda...When this happens to me, now and again, I start the engine with the cap off the radiator and then stand and watch to see when the level in the radiator upper tank goes down and then I pour more liquid into the upper tank...It usually takes a bit of time and the system will bubble and then the level in the tank will drop away and I will add more liquid. This can happen several times until all of the liquid is back in the radiator...Good Luck...Ernie

There's a tool for that. Pulls vacuum and removes the air. You trap air as the coolant enters in pockets in the block and they have to be released/filled. If you run it and monitor, you're running with hot spots as there's no coolant in those areas.
You can do the same with a radiator pressure leak tester. Just don't pressurize these old radiators more than a few psig.

I did as Ernie suggested, the water never went down so I can add more. I drove it 15-20 minutes and parked it. As Fishn Jim said I'm afraid the engine will get hot if I drive it more. I haven't taken the thermostat off the head and placed it inside the housing yet so I will empty more coolant out when I do that. Perhaps when the thermostat is where it belongs it'll use the right amount of coolant. I have a gallon left that won't go back in. The temperature gauge on my dashboard reads cool.