The only other wires that I can think of that are in that area are the secondary O2 sensor wires... perhaps something melted back there.
I know when my car sat for a whole winter, it misfired like crazy upon restart but new plugs resolved that for me.
Trying to think outside the box...Was the exhaust coming out the tailpipe reasonably well? Rodents could of gotten up there... don't put anything past those little monsters
How was swapping the starter with the supercharger in the way?
Dinan CAI &Throttle body, ESS Tuning TS2, Bimmerbrakes gen3 headers, UUC SSK & DSSR. Achilles oil pump, VAC oil pan baffle
M3 Motor mounts, UUC Trans mounts, Modified clutch style LSD 3.15, TMS front subframe reinforcement, Koni Yellow sports,
H&R sport springs, UUC sway bars, BMW Perf. Rotors, UUC SS brake lines, Hawk HPS pads, CSL replica wheels,
Rotora strut bar, FXR HID conversion, M3 Mirror conversion, BSW stage 1 speakers