When running 48 ida's, with velocity stacks, is there a benefit in running a taller one, rather than a short one? And I mean in terms of performance, rather than fit or looks?

"With no modifications, these "bolt on" stacks will increase flow by a 21 CFM over stock."

http://jayceevw.com/webers_by_jaycee

Yeah, they sound good on paper, but in reality the biggest restriction is the intake port and valve, by far. A bare carb may pick up 21 cfm with those stacks (or that could be just the stacks alone, hard to say where that number came from...), but by the time they are on a manifold and a head you would be lucky to pick up a cfm or two. I know Darren has never seen any dyno gains with these type of stacks.
The only thing you may stand to gain with longer or shorter stacks is in the harmonics of the intake, but that doesn't have anything to do with flow numbers you would see on a static flow bench...
I run them because they look cool and at least don't *hurt* performance.

So if they flow the same, why would they sell two different heights? Looks?

With my setup, short manifolds, etc. Which would you run? Short stacks to ensure clearance?

Like I said, if you know what you are doing you can do some harmonic tuning with the different lengths, but most people don't know about that, except maybe in simple terms. The rule of thumb most people know is longer for torque, shorter for horsepower. Beyond that I think most people probably think those huge, long stacks look "racy."
The ones I run are stock length. I wouldn't run the long ones unless I did the harmonic calculations and found I would benefit from them...

I don't know yet, don't buy them yet...