Angels Cartel/Minmatar/Rogue Drones: 2x Invuln, 1x Explosive
Serpentis/Gallente/Mordu's Legion/Caldari: 1x Invuln, 1x Kinetic, 1x Thermal
Blood Raiders/Amarr/Sansha's Nation: 1x Invuln, 1x EM, 1x Thermal
Guristas Pirates: 2x Invuln, 1x Kinetic

Valkyries/Zerks for Angel missions and Hammerheads for everything else.

Main Damage types to use on npc factions:

Blood Raiders-EM/Thermal
Rogue Drones-EM
Sansha's Nation-EM/Thermal
Amarr Empire-EM/Thermal
Minmatar Republic-Thermal
Angel Cartel-Explosive
Mordu's Legion-Thermal/Kinetic
Guristas Pirates-Kinetic/Thermal
Caldari State-Kinetic/Thermal
Gallente Federation-Thermal/Kinetic
Serpentis-Thermal/Kinetic
Mercenary-Thermal

Use a range script for targets farther out than 20KM and a tracking script for anything closer.

For vanguard sites, you may consider switching 1 or 2 Tracking Computers for Stasis Webifier (Faction Webs recommended for its extra range)