When you replaced the alt, did the pigtail wires to the alt get switched? If the exciter wire got switched to the sense side of the alt connector, it will appear to charge but when it's not running, the sense wire will ground internally in the alt and the battery will go dead after a few days..... like you are describing.
The sense wire is tied directly into the elec system and ends up at the pos terminal of the battery (allways hot). It tells the alt to produce more or less juice depending on the demands of the system.
The exciter wire is tied to the idiot light on the dash, when you 1st turn on the key the idiot light gets 12v from the dash side of the system and gets it's ground from the voltage reg inside the alt..... light illuminates. After the car starts the internal voltage reg removes the ground and starts producing juice...... light goes out.
If the wires were switched, when the engine isn't running the internal reg will ground out the sense wire that's tied directly to the battery. If this is happening the alt will get extremely hot to the touch when the car has sat for a few hours...... almost too hot to touch.