The S197 chassis is more refined and feels slower than the SN95. Automatics often feel slower than manuals. How it feels and how it really plays out at the dragstrip are often quite different, though.
I've owned a 2000 Mustang GT Coupe (manual), 2003 Mach 1 (manual), and 2007 Mustang GT Coupe (automatic), so I can tell you from experience that the SN95's felt faster than my 07. OK, the Mach 1 was faster, but the 2000 GT felt quicker even though it wasn't.
I flogged all three Mustang frequently at our local 1/4 mile dragstrip. The '00 GT ran consistent 13.90's and 14.00's with just 260hp, 3180 lbs, and 3.27 gears. The '07 GT runs consistent 13.30's and 13.40's with 320hp, 3450 lbs, and 4.10 gears.
Now, take a stock S197 GT AT with 300hp and 3.31 gears, and it'll run high 13's in the 1/4 mile. A lightly modded SN95 GT Manual ought to run mid 13's or better. So, dbrufus1234, if this is like your scenario with your friend, then his car is likely faster than yours, but not by much.