To answer the question: I’d be wary of using an Attack Battlecruiser such as the Naga for Level 3 missions - they have very low defences, and while the big guns can hit things hard they are really best operating at range. A MJD fitted one may work, but it could start feeling really awkward really quickly - jump to range and hope you can kill enough before they close you down while the MJD is re-cycling.
Anyway, as a reference, I’ve happily run Level 3 Security missions in Amarr space with a Ferox:
[Ferox, TES Abider]
Damage Control II
Tracking Enhancer II
Magnetic Field Stabilizer II
Magnetic Field Stabilizer II
Large Shield Booster II
Adaptive Invulnerability Field II
Adaptive Invulnerability Field II
10MN Y-S8 Compact Afterburner
Optical Compact Tracking Computer
Large Shield Extender II
250mm Railgun II
250mm Railgun II
250mm Railgun II
250mm Railgun II
250mm Railgun II
250mm Railgun II
Small Tractor Beam II
Medium Capacitor Control Circuit I
Medium Capacitor Control Circuit I
Medium Ancillary Current Router I
There are probably better set-ups - it does have weaknesses.
NPC Frigates are a real hassle - you will need to carry a flight of light drones for those if they get close; otherwise target them at range and pop them quickly. In the Level 3 missions, then the frigates will start to target your drones so keep an eye on them.
You can probably de-rate it if your skills are insufficient - drop some of the modules down to Meta rather than T2. The tracking computer is there to give you a chance to hit things - you’ll normally want a tracking script in it. Railguns have reach, but track poorly (try Minmatar Artillery - that’s really painful). The Tracking Enhancer helps quite a bit.
You’ve got a balance between an active and buffer tank; the limiting factor in active shield tanks is normally the Capacitor, so this gives you chance to trade a buffer for killing time. I’ve not normally struggled - though Angel Extravaganza is always a grind. The Tractor Beam is optional - I use it for gathering wrecks to loot.
I’ve a motto: There may be better, more optimal ships (so everyone buy a Machariel lets make life all same-y and boring) but flying something you want to fly and succeeding with that is more fun. It’s not just about the ISK/hr. If It was, then My Credit Card beats your Machariel.