Sounds like there may be a short somewhere, putting a parasitic drain on your batt. I would start looking for any damaged wires or connections on the truck. Could be anywhere. You might wanna swap the alt. though since you already have a replacement. If that doesn't fix the problem then at least you can cross that off the list and look elsewhere. swapping the alt. shouldn't really take to long. I remember mine was pretty easy.
2003 Ranger FX4 level II. 3" BL, 33x12.50 GT Radial Mud Claws, Custom front and rear bumpers with winch hookups, custom flatbed, with hi-lift, and full size spare mount, 12,000 lb winch mounted under bed, Electric fan, and of course a flowmaster.