Did you replace the alternator with an aftermarket alternator or a ford ot motorcraft alternator?
The alternator on your vehicle is controlled by the PCM and we have seen many after market alternators not work with this system especially the Delco ones for some reason.
Basically how your system works is after the engine is started, voltage is applied through the I circuit 1931 (BN/PK) from the powertrain control module (PCM) to the generator. This turns the regulator on, allowing current to flow from the battery sense A circuit 35 (OG/LB) to the generator field coil. When the engine is started, the generator begins to generate alternating current (AC) which is internally converted to direct current (DC). This current is then supplied to the vehicle electrical system through the output (B+) terminal of the generator. Once the generator begins generating current, a voltage signal is taken from the generator stator and fed back to the regulator internally. This voltage feedback signal (typically half the battery voltage) is used to turn off the warning indicator.
With the system functioning normally, the generator output current is determined by the voltage of the A circuit 35 (OG/LB) which is compared to a set voltage internal to the regulator. The regulator controls the generator field current to maintain the current generator output.
The set voltage will vary with temperature and is typically higher in cold temperatures and lower in warm temperatures. This allows improved battery recharge in the winter and reduces the chance of overcharging in the summer.
Now the best way to test and see if your alternator is actually functioning correctly on this vehicle is to hook up your meter on the battery.Start vehicle and run it at about 1500 to 2000 rpm's for about 10 seconds to initialize the alternator then unplug the 3 wire connector on back of the alternator with engine running. You are looking for 13.5 volts plus or minus a couple of tenths. If you are reading say 14v or more or 13v or less your alternator is bad or will not work with this system.
If this reading is ok then check your connections good and check the voltages at the alternator connections. Here is a chart for this
Normal Charging System Voltages and Charging System Warning Indicator Operation
If all of this is ok you will need to have it checked by someone with a scan tool that can perform charging system test.