I believe that 3.73's or 4.10's will have no negative impact on top speed on most cars Stangs out there. AOD or 5-spd, top gear is SO LONG that very few have enough power to pull up to their power peak in top gear. With more gear, most are able to actually use 5th or 4th in an aod as a top speed gear because the engine will come closer to reaching it's power peak with the lower gearing. Unless the car's pushing well over 300-350HP, the steeper gears will actually help top speed. It's the same phenomenon that allows a new Vette to hit its top speed in 5th gear instead of 6th. It doesn't have enough power at the rpm it's turning in 6th to overcome the aero resistance. Raise the rpm some, and it would go faster in 6th than it does now in 5th. It's true for any car that is aero limited instead of redline limited - and all stock stangs, and most modded stangs are aero limited, not rpm limited.
Disregard if you've got enough motor actually push the longer gears up into the power range of the engine. But it's usually the boosted cars that can do that - if you're normally aspirated, steeper gears (3.7, 3.9, 4.1 range) will probably help your top speed. For most Stangs (and my car too) considering more gear than stock, the up side - more top end, better around town mileage, better acceleration everywhere; Down side - more wear/tear on engine, slightly worse highway mileage.