The JDM ITR will give you the best acceleration, but you'll want to pick the transmission that allows you to reach the end of 4th gear by the end of the strip. If you're running a beefed up B block that will require you to shift to 5th before you run through the 1/4 mile, you might want to go with the USDM ITR. Of course, you can always fix that problem with taller tires....
How much money are you willing to spend? If you're going all out, get the JDM ITR and run taller slicks to get your final gearing right.