While anything is possible, the stock tires will likely not be sticky enough to run 12.40's with just a 100-shot. Even on drag radials, that would equate to a high 12 second car - not a low 12 second car - so I would guess 12.70's at best for a 100% stock GT with a 100-shot if you got really lucky with traction.
For comparison, my 07 GT runs 12.30's with a 150-shot (supercharger, not nitrous), 4.10 gears, big converter, and drag radials. On factory tires, I would be lucky to run high 12's (although I've never tried the blower at the track with factory tires).