I don't know squat about John Deere but I know that Diesels with a HPFP can be very sensitive when it comes to filters and filter housings. I'd check there, Thoroughly, and work from there. Diesels require three things to run - Fuel, Air and Compression. The HPFP (HighPressureFuelPump) is a wonderful invention but it brings certain headaches with it. It's why they go for $2,700 new. On your tractor
Make absolutely certain you're running an OEM fiter and check the housing for cracks or leaks. I've seen more problems with aftermarket filters on diesels than almost anything else. Except for maybe the emissions garbage, which you shouldn't have much of anyway. If at all.
Good luck.