There are a few key differences between long tube and short tube headers. First off, short tube headers are typically easier to install, can bolt up to a stock exhaust and in many cases are 50 state emissions legal. Long tube headers will require a new, shorter h-pipe or x-pipe to connect the exhaust between the headers the the mufflers. Long tube headers also tend to be a little louder than short tubes.

As for power, there is no easy answer. Shorty headers are usually better for cars making less than 350 horsepower. Long tubes will make more power when you're looking beyond 350 hp. Below is a link to a great article in 5.0 Mustang Magazine that tests shorty and long tube headers on a Mustang just like yours.