Ok, so, you're looking for something in the "catastrophic failure" category instead of a general cooling mismatch then. I assume you checked the coolant level.
You already replaced the thermostat and you can see water circulating in the radiator, so, the thermostat probably isn't the issue. But, what temperature is it and did you test it before install? If it's not opening all the way it could be restricting flow.
Next would be to check if the lower hose is collapsing, if there was a spring in there before it could have rusted out (old ones weren't stainless). Then the water pump. You're circulating water, but if there's something going on there you might not be circulating the amount you need- bad bearing/shaft would reduce water and air flow. You also say the clutch fan is working, but what type do you have? If it's not spinning fast enough you could be losing air flow. And of course something could have broken loose in the engine (big old chunk of RTV, or rust, or...) and plugged something important.
I would just start checking the general condition of things. Hoses, belts, play in the impeller shaft, do a coolant flush on the radiator, that sort of thing. Looking for stuff that's worn out, out of place, etc.
