Okay, my turn.
First of all, like many others have already stated, this is gonna be a close race (both 5 speed manuals). However, I'm gonna have to put my bet on the 88 GT b/c:
1) Lighter
2) 5 speed manual (if it were AOD, it'd be different)
3) 3.73s
4) Other minor mods.
This is all assuming EQUAL driving skill. Now I have to say I COULD imagine it like this:
Both come off the line at the same time, but the 88 GT gains about 1/2 car length through 1rst and 2nd gear. Then at about mid 3rd gear, 2001 GT starts reeling him in and by 88 GT's 4rth gear, 2001 GT has him by a front bumper.
I'm still placing my bet on the 88 GT though.
(but it's hard to ******* tell b/c I haven't seen Mad Horse's GT run. (arrgh)
Don't screw up
Mad Horse 
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'79 Mustang Coup
4" Cowl
Weld wheels (15x6;15x8)
Stock 5.8L
C4 w/ shift kit
1 5/8" MAC shorty headers
Holley 750 CFM
Edelbrock Performer RPM intake
2.5" Off road H-pipe, 2-chamber Flowmasters
8.8" Rear end w/ 3.55 gears (Now that's more like it!!)
Front: 225/60/15 Rear: 255/60/15 Eagle GT II
14 x 4” K&N air filter (getting the Xtreme setup soon)
"Red, thou art my companion. Hasten now your quickened metamorphosis to Green that I may conquer all who dare abide there beside me. May they be left thither behind burnt black." ---Fox Body