Try shifting at 6500-6700 RPM. See how your times do then.
How quick can you shift, and how where you shifting? Grandma, speed, or power?
I have a 2000 GT (Check Sig) and when I race (Street) I usually ring her up to 5700-5800 RPM and speed shift (My friends say if they didnt know better theyd swear I had an Automatic cause I shift so quick

)
WIth a 99+ GT I found that if you dont run second gear up to 5700 + RPM, your third gear accerleration kinda suffers. Well thats a GT, not a Cobra like you have, Lucky Dog.
EIther way, glad to hear you had fun, thats whats its all about FUN.
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64 1/2 "D" code Red Mustang Coupe. 289, C4, Mallory duel point. Ported & Polished 65 heads shaved .01 with 351 valves, 11:1 comp, 1.7:1 rockers, blue wolverine lumpy cam, modified 4100 Hipo 4 barrel. GT Apperance pkg. And to many others to list
2000 Perf Red Mustang GT. 5spd. BBK Underdrive pulleys, Flotech off-road H pipe. Hurst T-Handle, 40 series Flowmasters, Steeda Tri-Ax. Ordered 4:10's.
64 1/2 red 6cyl coupe. Future resto.