Small update. We were waiting for a new fuel tank to arrive which took a while. I dropped off the tractor on the 15th and they are still working on it.
Turns out the new tank has the exact same marks which looks like cracking, so it is a form issue.
Regarding the regen, the EGR valve has been replaced, and the injectors have been checked and are operating normally. The software was also updated.
They are going to change the thermostat. I was driving and couldn't take notes when we spoke, so my numbers may be off, but as I recall, my tractor was running about 168 degrees, it takes 155 degrees for it to go into regen. Running a little cool, seemes they like to see them between 180 and 200. I live in AL and even working it in 100 degree WX, the temp gauge never rises above 1/4. So hope getting it to run a little hotter will help with soot production along with the other stuff they did.