The lightning is a great ship. Let us first assume you don't want to use any plug-ins. Your configuration is good, however I would do the following:
I would keep the primary configuration you have. Lasers are great for Monty Pythoning, throw in the proton to fill out the primaries. This should leave you with 70 tons to play with. The way you will run down enemies is by using your high recharge to your advantage, so add a shield booster (2 tons). Add the three engine upgrades and two detector upgrades. For defenses add a missile jammer, flares (1 ton), afterburner (5), and thus a ramscoop (5). Now you have 57 tons left.
Depending on what you want to do, you could add a turret (20 or 30 tons) and armor (5, 10, and/or 40 tons) to maximize your frontal assaults or put in 1 torpedo launcher (25) and fill up on torps and durasteel or armaplast.
Alternatively, you could put in a Hawk Bay. Normally , these are useless, however if you continuously launch, target, and recall them without ever letting the fighters engage you have an unlimited supply of free missiles. This is 50 tons--the same as you are using on missiles now.
The point of whether a fighter should have a fighter bay is an entirely different one. 
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