That must be very frustrating.
You need to be working through this methodically. You might very well be and it isn't coming across well, so forgive me if it seems like I'm attacking you.
A couple central dogmas: 1. The radiator and cooling system as a whole function to manage the excessive heat in your diesel engine. It should be neither too hot or too cold. 2. The cooling system as engineered and installed by Yanmar originally will allow the engine to output its maximum rated power essentially indefinitely without overheating.
Given those two truths, we can make a conclusion: If the tractor overheats, it is not installed as it was originally. That is, something has changed. We need to do detective work to isolate where/what exactly the difference has occurred.
I like to start simple, and work toward hard, and cheap toward expensive.
We have a glaring problem with the the leaking cooling system. That wasn't present before, apparently, so it must have happened as a result of re-assembly after the radiator was replaced.
If it is coming from the water pump area, there are essentially two options, assuming the pump wasn't removed: a) The seals in the water pump somehow went bad in the few days between pulling the radiator and now, and chose this precise moment to start leaking. This is possible, but not especially likely; mechanical devices tend to not magically "go bad," but to be fair seals are among those that might do so. b) The re-assembly is not correct, in alignment/sequence/intact components. Since "a" is unlikely, let's pursue "b."
In the diagram from water pump housing up, there is what looks like an O-ring, the thermostat, then a gasket, and finally the top hose mounting elbow. Are those parts on, in that order? If so, are they intact, correctly aligned, and properly torqued? Is the hose itself cracked? Is it fully seated over the elbow? Is the hose clamp properly attached? Don't fall into the trap of smearing silicone or other sealant everywhere: Remember, our central dogma is that if we put it together as Yanmar did, it's good for 30 years or more. Until logic dictates otherwise, we should always revert to the original configuration.
If you have found a simple fix, go ahead and correct it. If you have not, and everything appears correct, go to the auto parts store and rent a radiator pressure tester (If you don't still have the earlier one). It fits onto the radiator and allows you to pressurize the system. With everything assembled correctly, pressurize the system, and isolate the leak's location. If it is from the water pump's weep hole, then the seals will need to be replaced. If it is from a cracked thermostat housing, repair that. Etc. Etc. It may be helpful to write your own dichotomous key (the yes/no part to isolate the trouble) before your start down another path.
Use water instead of coolant in this process, if you haven't already done that. It's cheaper and less hazardous across the board. Then once you get it figured out, drain and fill correctly.
Work in baby steps, simply and rationally. There is a hole between the inside of the cooling system and the outside of it; you just need to figure out where.
Good luck, let us know how you do!