Need help for a stalling 94 chevy 6.5L diesel turbo

I'm working on a 94 chevy silverado 3500HD with a 6.5L diesel turbo engine.It is a cab and chassis with a custombuilt hydraulic flatbed. The engine stalls intermittently and registers a code 35 which is an injection pulse width error. Scanner reads 1.8ms pulse width at an abnormally high idle speed of 1100rpm.While doing a pin voltage testing, I discovered that pin A6 of the ECM was hotwired to ignition. Schematic diagram reveals that there should be no connection to A6. Removing the B+ to pin A6 dropped the rpm to 700 rpm and injector pulse width reads 1.77ms but engine still stalls, specially while accelerating and immediately after  service engine soon light comes on with a persistent code 35. Is the connection of A6 to ignition acceptable and valid modification apparently to raise the rpm  to boost the hydraulic pressure for the towtruck's flatbed? Has it caused a potential damage to the ECM causing the engine to stall intermittently? Are there other usual possibilities causing the engine to stall? Likewise, is there any suggestion for a compatible aftermarket clutch kit. Clutch disc wears prematurely. Your technical advise is greatly appreciated.

Has 1 6.5 liter that would run like **** when it got warm, would smoke lots as well, no power and die.  Ended up the intake manifold was cracked.  Maybe something to check??