Your argument is flawed. Your 03 GT may run 13.30's, but it is far from stock. I owned a 2000 Mustang GT 5-speed coupe that ran a best of 13.85 (and a back up run of 13.87) bone stock on the factory tires. Ran mostly 13.90's, though, wiht the occasional 14.00 depending on weather and traction. Most 99-04 GT 5-speeds ran high 13's to low 14's bone stock. My 00 GT weighed 3180 lbs per our local DOT scales.
My 07 GT Coupe is an automatic car (180 lbs heavier than a manual) and weighs 3,530 all stock. Bone stock S197 GT's run mid 13's (manuals) to high 13's (automatics) in the 1/4 mile, so while they weigh a couple hundred pounds more than an SN95 GT, the extra 40hp more than overcomes the weight difference. So, stock vs stock, the S197 GT is quicker than the SN95 GT.
Now, my 07 GT Coupe is lightly modded (see sig below), but has run a best of 13.32 @ 102 in the 1/4 mile on the factory tires and 13.28 @ 102 with drag radials. So, my heavy S197 GT Automatic is just as fast as your moderately modded SN95 Manual.
Seems like you are flawed too, I've seen DR's wipe off .5 on the strip, you on the other hand lost .06
Plenum = 2~hp03 sb 2v 5spd:13.38@104,Trick Flow intake plenum, steeds u/d pullies, upr x pipe, flows,FRPP 3.73s
UD's = 5~hp
X-pipe = 6-7~hp
Flows = 0hp
You have a tune w/ higher octane, higher gear, your stall makes up for the auto to manual difference..Best Drag Racing: 1/4 mile, 1.83 60' and 13.28 @ 101.92 mph.
Mods: FRPP 4.10 gears, 3800 rpm Stall Converter, Diablosport Predator 93 Octane Tune, CDC Sequential Taillights, Redline Tuning Elite Hood Struts, etc.
Ok he spanked you on trap speed, which means he's faster, he is putting down less power and is faster than you
99-04 are close to 3400lbs
05+ are closer to 3550lbs