The wiring they're talking about is the solder joints inside of the plug (afm side) where they go to the little PCB, these get old and dry and are notorious for cracking.
Running a valley cover or not is up to you, I prefer not to so it keeps the coils cooler. The igniter is earthed through the loom (look at the ECU side of the igniter, that plug should have an earth lead that pops out of the harness and earths to the rear coil cradle bolt), I bolted my igniter back to one of the valley cover bolts, works fine.
AFM dying shouldn't cause it to stall.. I thought it would just try to go into a limp mode when it cuts out.. the ECU will make a "best guess" to keep the engine running so you can limp it to a workshop..