By raising the number of the gears in the back you are increasing the torque multiplier to the wheels making it easier for the engine to turn the wheels which allows you to "rev up" quicker. Now granted, RPM for RPM you will see a slower acceleration... but the increased torque multiplier factor by your gears more then compensates for this.
Grr... I hate explaining something like this. How's this... if you go from 1,000 to 4,000 RPMs with a stock gear set you'll be going about 30 miles per hour in first gear... with the 3.90's you may only be going 25 or so miles per hour which is slower... but you will have been able to get from 1,000 to 4,000 rpms much faster making the acceleration better.
Now one things about the 3.90's... Ford racing doesn't make that gear set... you have to get the others (Mopar is it??)... from what I've heard they're just as good quality wise, but the install is a bit trickier... apparently any monkey with a wrench can put in the Ford gears without noise but the other gear set requires a bit more finess...
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