Re: New Batteries and Alternator...still not charging.
Did you recharge the dead batteries with a dedicated battery charger or attempt to charge them with the new alternator? The latter procedure is not recommended and frequently will burn out the voltage regulator in the alternator. There is a fuse link in the wire to the battery (goes to the passenger side battery). If this fuse link blew, the alternator may be putting out the juice but it is not getting to the batteries. Use a continuity tester to make sure this connection is intact. If the connection is intact, charge the batteries, and take to your local autoparts store to test in the truck or remove the alternator and have it tested where you purchased it. It must be in warranty.
2002 F350 Lariat CC 4x4 Auto 4.10 DRW, DP-Tuner F5 live tuned stock, quiet, 40dd, 40, 60, 80 tow, 80e and 120r, B&W GN, BrakeSmart, 'pooned tank, tank and pre-pump mods, 2µ Dahl 100 filter, regulated return, BTS dual HPOP, AC singles with EDM 34 lpm nozzles, AIS, H2e, Spearco 6.0 IC, Hypermax 3.5" dp--> MBRP 4" 304SS exhaust, BTS tranny, 203º T-stat, Chevron ELC, coolant filter, Oilguard bypass with Schaeffer 9000, WranglerNW 200 amp alternator & Optima group 31 batteries, Nippon-Denso starter, SPA gauges, SteveRacer mods, Hella 80/100W 9007s, Hella Micro DE foglights, 1000FF driving lights, 220W backup lights, Stancor contactor, Michelin XPS Traction tires, X-Springs, Bilstein shox, custom bumpers but otherwise stock. Nov 30 '99 build engine with 16 K miles, Fluidampr, Comp Cam 910 springs, Melling LPOP and ARP headstuds.