I have just solved this exact problem with new coil boots; and the wiring harness is bad but still functioning. Diagnostic tester revealed misfire on #6, fixed with new boot.
Easiest way to tell the harness is falling to bits is to look at the wiring at the 3 connectors that run under the removable black plastic cover attached to the front of the valve cover. I think one of these plugs is attached to the cam magnet (?) the other two run farther in. The insulation on the wires (under the outer black sheathing) will have hairline cracks running all around them. If you move 'em around too much its starts to flake away, very nasty.
1995 MB E320 Wagon
2001 BMW 530i
2007 MINI Cooper S (!)