What todd said, a new battery sounds in order, that fan no matter how big it is or how many amps its drawing should not drain a battery in that short of a time.
Also, if the alternator wasn't done right, take it back???
OR
Bite the bullet and just buy a brand new hi amp alternator.
Another suggestion would be to install a bypass switch so that when you turn the motor off, you can turn the fan off.
To me, that would be the simplest thing to do :roll:
Goodluck, Cp