The truck really needs to be hooked up to the DXII software to get an accurate diagnosis. Start with this.
It sounds like you lost the range switch on the side of the transmission where the gear shift shaft goes in. Water gets in these switches and messes them up.. There's an updated wiring...
It is normal for those to do a regen every 100 or so miles. You're within the normal range. Do you ever have to do a manual regen? If you do, how long do they take?
Update: water can get into the firewall junction box from a leaking windshield seal. If it gets into the CAN wiring, all sorts of weird things happen. The junction box needs to be opened up and inspected for water.
I don't know if they're the same or not. There was a big step up in emissions stuff between those years. The VNT controller is calibrated to the turbo at the factory, so swapping controllers often doesn't work correctly.
Unfortunately Hino doesn't give out much oscilloscope data, so I can't help you there. It definitely sounds like a low fuel pressure issue, and you've already checked the rail pressure limiter.