1. The main pump to the common rail will not show much flow. The high pressure pump is made to create high pressure, not high flow. Very little fuel will be seen from that line. For general diagnosis and testing, there is no need to remove that line.
2. The primer pump will stay on, that is normal.
3. Active codes will be displayed in the dash, reply with those.
Did the turbo shaft have any play in it? Was there any oil in the air intake or exhaust? The turbo is a very weak point, and you really need to look at it closely. Spin the shaft and feel if its rough. Any oil will indicated it need to be replaced. I know that it is hard to reach, but make sure you check it very closely.
The harness has multiple wear points, and rubs through. Some common rub points are :
1. Rear right of machine, harness section going over the ac lines/ near the ac lines **<----look VERY close there
2. Harness above left drive motor
3. Around/behind the cab fuse block.
Update when you have the fault codes.