This kinda depends on many variables. Such as, what kind of roles each ship fulfills in bounty hunting, how many ships at once you plan to engage, whether you are looking to fly solo ore wing up?
There's no "One Build to rule them all" (thank the lords) but there are mods that aid in certain roles, for example shield booster mods to increase resistance to certain damage types, or shield regeneration mods that allow you to recharge a wingmates shield by firing a beam laser at him/her.
For damage output there are mods that increase heat levels within the target ship causing internal damage to their modules, often resulting in multiple malfunctions.
There are even modifications that simply decrease heat output of your own weapons, potentially allowing you to fire them longer without risking damage to your own systems.
Take a look here and decide for yourself what you prefer
http://elite-dangerous.wikia.com/wiki/Engineer's_weapon_special_effects
Sorry I can't be more specific, odds are that others will jump in with their own suggestions but in the meantime I hope this helps.