The truck is a 2008 Ram 2500. The emissions system is mostly deleted (the ccv filter and tube are still present). The exhaust manifold is a BD 2 piece unit for a 5.9 along with an Industrial Injection turbo. The intake horn is a GDP unit.The tuning is done using an XRT Pro.

The problem:
A week ago the CEL came on and when I pulled the codes I found it to be P0341 Cam Position Sensor. I figured replace the sensor, problem solved. So I replaced the sensor and cleared the codes using the XRT. The P0341 code came back with a friend. I checked it again and came up with more codes.

The codes were as follows:

P0193 Fuel Rail Pressure Sensor Input High
P0341 Cam Position Sensor
P000F Fuel system over pressure, relief valve activated
P0087 Fuel Rail system pressure too low
P0652 Sensor Reference voltage b circuit 5 volt
P0192 Fuel Rail Pressure Sensor Input Low
P0107 MAP sensor circuit low
P2228 Barometric Pressure Sensor Circuit low

This led me to believe the issue was in the wiring. Sure enough I found a wire bundle on the driver's side near the crank position sensor that was rubbing on a hard line and had worn through the insulation on one of the wires. I resealed the wire using RTV and zip tied the wire bundle up and away from the hard line.

This fixed all but the P0193 code and the charging system light (lightning bolt on the dash) is still on. I just put two brand new batteries in the truck so I'm fairly certain that batteries are not the issue.

I've tried to clear the code multiple times only for it to come right back while the key is in the run position without the engine started. There is a very distinct knocking noise coming from the engine compartment when I try to clear the code, almost as if an injector was attempting to fire.

any advice would be greatly appreciated.