If money isn't an issue...then I wouldn't hesitate to get the full size.
It cools better, less chance of heat soak.
Allows more pulley drop.
It lasts longer and is thick enough NOT to warp like the short stack, etc....etc.
It's worth the $400 difference, not to mention the fact with injectors and a custom tune you'd be running a 3.0"~ on basically a stock car vs. a 3.25"-3.3" with a SSIC setup.
Money really isn't the issue. I was just looking at installation problems. If the short stack is just going you warp over time then obviously thats a no go. So is there any problems (long term) with the full size ones?
It's been four years since we put your intercooler on?
-_-