+100%
You can have a safe out of the box tune, but you would have to run richer and with less timing. Much like the OEM tune that is very safe, but leaves a lot on the table. To get the best tune, you have to dial in the MAF transfer function for your car and confirm the A/F ratios and timing for your particular car and gasoline combination. That would optimize your GT for moderate to hard pulls on street, strip or dyno. The next level of tuning to optimize idle, part throttle and transitional throttle movements. That would take more time on a load dyno and or street tuning while data logging with a wideband O2. After this area of operation is adjusted you can choose to work on adaptive learning next. Most tuners, if not all, prefer to leave adaptive learning off. Adaptive learning allows the ECU to remember optimum closed loop A/F ratios and to store them in KAM (memory). The problem with adaptive is that it learns corrections during closed loop (part throttle, usual less than 1/3) operations and may apply the corrections to open loop WOT operation. That can be dangerous at WOT if you don't have the lower portion of the MAF mapped near perfection. The benefits of adaptive is during transitional throttle movements in closed loop operation, the ECU zeros in on the correct A/F ratio quickly leading to slightly smoother operation. Also the ECU can adjust for seasonal gasoline variability, such as ethanol content. In my area ethanol can vary from 0 to 10% by volume!
Unless you are a techno geek with a lot of spare time, I suggest you find a knowledgeable tuner with experience with blown modular Fords to get a dyno/road tune, otherwise look look at these web sites
http://www.sctflash.com/product_racer.php and
http://www.innovatemotorsports.com/products/lc1.php to learn more about how to spend more time tuning your GT rather than driving it.
Those of you near Torrie, or TonY G, should without a doubt start there.
p.s I am still fine tuning my GT! It never seems to end.