Saying crack instead of hole sounds like running into something or something having dropped on it as opposed to a stick punching a hole in the radiator. Is it possible this damage occurred during transit or even existed prior to them selling you the tractor?
Where is the crack in the cowling-- e.g., on the front like the tractor was run into something or on the top like something was dropped on it from above?
Is this fresh damage that appears to have happened recently?
Others can correct me, but I tend to use the level of coolant in the coolant tank as showing me how much coolant is present. I rarely take the radiator cap off. What does your owner's manual tell you to do about checking the coolant? Does it say to take the rad cap off?
I'd be asking them how much the coolant was low and when did they determine this?
If it wasn't knocking before you took it in, did the dealership do something to cause this?
You also mentioned the lack of a guard. Not sure what you are asking, but apparently a lot of tractors are sold with a grill guard frame that doesn't have any mesh on it to prevent sticks from poking through the cowling. They might or might not sell an accessory mesh insert for the grill guard frame.
40 minutes of regen seems unusually long. I thought regens usually took 20 minutes? Does your owner's manual state any expected time for a regen to be completed?