So I have never done a John Deere, but I do a ton of cat. If I had only these three codes left, I would pull the def injector and run a def injector spray pattern test. Not sure what it is on your program but might be under bidirectional tests. You wanna see a nice cone shaped spray pattern so that the def atomizes into the mixer housing. While it is out, check inside the hole for def crystallized.
Have you already run a few regens? Maybe it has a different name like aftertreatment test.
Cat won’t let you run with active codes, but those look stored and might be able to be cleared so you can run these tests.
Worse case you will pull the scr and clean it. Little bit of labor but I think it should clear everything. When I run into these issues and have already replaced everything but cannot run any tests due to active codes, I just let it idle. Eventually the machine will sense it is working again and clear everything.
Good luck