Re: gear swap
I have not gone lower than 3:27's, which are stock in HPP cars, but have installed gears as low as 3:73's in Mustangs. The PCM was not affected, nor was the 4r70 in the CV. The Mustang was a stick.
You will lose your speed control if you go lower than 3:27, but your speedometer can be corrected. Check the current Ford Racing and Power Products (FRPP) catalog for the speedometer correction plug in. It electronically corrects the difference in your signal generator caused by the gear change, kind of like changing speedometer gears in older transmissions
As for the ratio that works best, it's all about what you want the car to do. 3:27's are a good compromise gear for performance and mileage in a daily driver, but of course, the lower the gear (3:55 or 3:73) the better the car will accelerate.
Your torque converter stall speed is also something to consider. You can run a "looser" torque converter with higher rear end gears and get the same 0-60 times as with lower rear gears, but still get fair mileage and top end in a daily driver.