I think my mother's '99 Cobra convertable pulled a 12.8 with the following modifications:

IRS swapped for a 8.8 live rear with 4.10's
Full-length BBK headers
High flow BBK cat H-pipe
Flowmaster exhaust
Larger MAF w/K&N
Under drive pullies
BBK throttle body (later taken off because it greatly reduces driveability)

I think that was it...hopefully Craig will chime in. He was the actual person to do most of the work and drive the car to get those times.