I would start by replacing the stock wires going from the alternator to the battery, the engine to chassis, and the battery to the chassis (the magic three). It doesn't matter what you upgrade or how powerful your electrical/charging system is if the wires that are already in place aren't capable of carrying the extra added current.
1992 Toyota 4Runner SR5 4WD (5 Spd.)
Pioneer DEH-P6500 Head Unit
Boston Acoustics ProSeries 4.5 Components (Front)
Boston Acoustics RX47s (Rear)
JBL P-80.4 Amp (for front's and rear's)
Boston Acoustics ProSeries 12.5LF 12" subwoofer
Alpine MRP-M200 Power Amp (for subwoofer)