My bet is you have a poor connection at either injector 2 or 7. When you lose the connection to 1 injector, the ficm shuts off the voltage to 4 injectors. It powers the injectors in 2 blocks of 4, and grounds the injector to activate it. The FICM outputs 48 volts for an lly, and 48 volts is enough to arc and cause all kinds of issues if the circuit is left open, so as a safety it kills the entire group. So that leaves you with 4 cylinders running, hence no power, and the 4 cylinders dead pumping make the exhaust obnoxious.
The only time I know of that the ECM kills pilot in the programming is when the main injection fuel rate drops below roughly 2.5mm3 of fuel. Many times excess engine noise results from high rail pressure. Pilot is still active, but due to the extremely high rail pressure, the injection pulse width is so reduced, cylinder pressures spike from the increased injection pressure, and clatter clatter clatter even though pilot is still there.
The harness rub issue by the alternator normally results in blown fuses and a no start. Without codes though, it's all guesses. Based off of what you've posted, I would get a can of electrical contact cleaner, spray out the plugs of injectors 2 & 7(front drivers side and rear passenger side), and do the ice pick fix(google lly ice pick, you'll find MANY results).
