Try cleaning the contacts on the alternator and battery, check the wires between the 2. check the connections at the fuse box(under hood) for the alternator. If a wire is frayed or melted, replace it. If you got a cheap rebuilt alternator, that may be the problem, they don't seem to last as long, though I did get lucky and got a rebuilt Mitsu one from advance auto once for my 2.6 and it still works great even after being water/mud logged numerous times

Eric
89 Raider V6, 35s, 5sp, welded rear, 8k winch
89 Raider 2.6 going on 84 4runner frame