Hi,
Does the engine compartment fuse block cover have a legend inside detailing the function of the fuses and the relays?
I think that there is a "charge" relay located there so was wondering if it was OK or not.
Try the following test and if it fails the test AND there is a charge relay check if there is another similar relay (same specifications printed on the relay) in the fuse block that you can temporarily replace it with and check the voltage at the battery again. Switch the engine off when changing the relay.
If you have a DMM (digital multimeter) use its' Voltmeter function to test the voltage at the vehicle’s battery when the engine is running.
Park the vehicle and firmly apply the handbrake (emergency brake), ensure that the transmission is in Neutral (MT) or Park (AT) and switch off the engine.
Open the bonnet (hood) and then start the engine. Then connect the Voltmeter across the vehicle's battery terminals and measure the voltage.
IMPORTANT!
Be safety aware as the engine is running - watch where you place your hands etc and beware of any loose clothing, hair etc that may get caught in the moving parts of the engine.
With the engine running there should be 13.8V DC - 14.5V DC across the battery terminals. If there is <13.8V DC then as you have replaced the alternator it may be a faulty charge relay? (if there) or a faulty voltage regulator. I'm not sure if the regulator is a separately mounted component or whether it is integrated in with the alternator though