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?