Long tubes. I did the shortys once, and regreted the hell out of it. I just did LTs, and I am a very happy camper, ah er Cobra driver I mean.
Totaly changes the tone. Nice at idle, screams like a rabbit gettin F***** by a Rhino at full Throttle. Gotta love it. Little more money now will make you happy later. You know deep down you want to do LTs........
LT's are better in every way, except when it comes time to pass emissions. And if it gets chilly where you are (and you drive the Mustang then), then you want to at least keep regular size crank & alternator pullies if you go with LT's. Helps keep them O2's toasty.
One of the magazines compared BBK longtubes agianst short tubes (equal and unequal) on a 400 plus hp engine. To my surprise they found very little difference between the 1 5/8" headers and if I recall right the short tube unequal headers seem to beat out all of them by a few HP. Now I have always heard LT are the way to go but after reading that I kept my shorties.
I did not see the referenced article. However, every test I have ever seen has pegged the long-tubes as far better for torque production (even if both were close on horsepower). I went with long-tubes and have been glad ever since.