I own a Kubota M9960 with a v3800-CR-TIE4 engine. It is

Dan, Let me try to explain. First, let me put a temp gauge in prospective to my explanation. Divide the gauge by tenths. lowest 10 is not even up to run temp. highest 10 is where engine boils water and you know it has to be shut down. The normal operating temp of my tractor would fall at 60-65% of gauge. this tractor has 1363 hours at time of major failure. We did a complete service at 1250 hours. engine oil and filter, fuel filters, grease where needed, checked belts, physically checked water level both in radiator by removing cap and overflow container. washed and cleaned tractor including all the cooling system, ac condenser, hydraulic cooler(sits in front of radiator), and radiator. We have daily checked fluids and blow out cooling system daily or in some cases we might be a few miles from home with only a ten or fifteen acre hay field to work. a few hours cutting, leave tractor there, rake and bale next day or so before coming home- less actual run hours than a complete 8-10 hour day.
So, about a two months ago on a field that takes about five hours to cut, after about four hours the tractor tried to do an auto regen while cutting with a 9ft disc mower on. the temp starts creeping up. within five to seven minutes its at the 85% and climbing mark at which time we pull out and go to shade tree. Ten minutes, idled down so regen stops and begins to cool. we start back cutting. same thing over again. this time we go to the nearest water source and gradually cool tractor so we can rinse cooling system. I had to sit for a hard regen for 45 minutes with temp getting back to that 80-85% range. when done, we finished cutting. over the next few weeks this similar situation has repeated itself several times. on the last day we had rolled 40 rolls of hay. temp just kept slowly climbing. Then as I finished a bale going up a grade the temp went into that top 90% mark and tractor boiled water and of course blew steam everywhere. stopped baler, idled down, moved 100- 150 feet into edge of field shade. It began to cool some and we shut it down. after it cooled for an hour or more, we checked radiator and added approx. half gallon of water which filled it up so it did not boil dry. cranked, finished baling another six rolls. loaded a trailer with rolls with front loader. Headed down the road to house, approx. 6 miles. DID NOT MAKE IT HOME. Tractor quit on way home and has not started since. Took to dealer. Kubota has had them do all the basic test and checks which is taking forever. They did a compression test that failed miserably. tech says compression should be in near 375 +or_.
#1 = 110, #2 = 16, #3 = 10, #4 = 324. pulled head where cylinder walls show scaring, worse in center holes. NOW, here we are. Obvious heat related failure. I know this, I do have some mechanical ability, just not a good diagnostic person. The expensive question----- WHAT CAUSED THE HEAT PROBLEM? and how long has this been going on? I can not help but believe that the regen system has been holding heat somehow for a long period of time. I just do not know where to look. And, the mechanic at the dealership is young- he may be good- but very inexperienced at diagnostics too. As in, he hooks up the computer and does what it tells him. Not real sure if he has had to determine the "cause of failure". Can you help?