x2, when the alternator died on the wife's RS, I ran the trooper back until the gage on the dash was somewhere less than 10 volts. I had to use an old charger, no problems. I have a red top in both Zus, and a yellow top in the previous F150/expedition/explorer for about 5 years. I had killed that battery several times with no problems.
I would guess you need to do the parallel charge trick, or just exchange it. My VX sat for almost 6 weeks for the tranny swap, and it started right up with no problems. Take it to autozone and they can tell you if the battery is bad...