Missions & Complexes

Since I don't know how to play the game I googled a fit from battleclinic: http://eve.battleclinic.com/loadout/25797-Hurricane-Dark-Fusion-Terror-L3-Mission-Runner.html

It worked pretty fine with crap skills and zero risk. BS might not be a good idea at L3's because the ships are so small.

AC's are faster when you have skills but for example the fit Goose99 linked requires all V skills to even fit. With meta4 guns & ab etc. it is easier but you still need to get 10km closer than with arty fit.

Republic fleet ammo is like 14x more expensive than normal ammo. When you get a few mil from a mission I don't think it's worth to spray crazily expensive low damage shells around.

This is a good fit, I've used it in 3's. I personally like the Drake for 3's though, easy mode with passive shield.

I think you're all over-thinking it. I have been doing level 3 Brutor missions in a generic, onmi-tank Drake forever, and rarely saw armor melted with all T1 (mostly mission loot) modules. Once I slapped on a couple T2 modules for tank, getting to 50% shields is rare. Only use T1 launchers and heavy missiles with a meta 3 TP I looted long ago, and weak T1 drone skills for frigates. Decent missile skills (4s and 5s mostly). Even the multi-room, multi-mob Extraveganza missions see maybe a lost drone if I'm careless. Missions that have me against the other race's navies fare no better.
I'm not freshly able to fly BC's, but all during my time running Lvl 3's and skilling up to this point- I've had to warp out of a mission room maybe twice, again with ALL T1 modules and a comically spread out skill build (certainly not uber at anything) . Maybe it's the Drake, but the standard agent missions are ridiculously easy in a tier 2 BC.
I can't speak to using a BS for a level 3, but given the make up of the NPC's- mostly frigs and a few cruisers/BCs - the BC is probably the better option. BS sized weapons would be wasted on virtually all the NPC ship types, if you hit the little ones at all.
If I spent the money on T2 launchers and ammo, it might use a few less heavy missiles per mission, but really isn't remotely needed and the T1's are cheap.
That's just my experience, but I've been running level 3's too long already and am saving for a move up to BS hulls, so I'm just a touch ahead of where the OP is at.

I found that running level III missions was a good place to pause at while I went back and trained up the more basic skills to the 4 and 5 level and start fitting T2 modules. Just a natural place to stop doing new things to fill out support skills to those multi-day investments to 4 or 5.

In the past couple days of actually putting a couple hours into missions, I made a 6mil isk wallet read 41mil (salvaging after missions) and lost two drones doing it. Usually while watching something on TV or eating lunch, so I'd say minimal stress in doing it too.

I've got an Invuln Field I and a DC II along with two LSE and need to start swapping my T1 low slot powergrid and CPU modules now that my skills are better.
YMMV, but a Drake with even half decent skills will walk over pretty much any standard mission. And again, I stress that I never fit specifically for the NPC's. It's LSE, IF I and DC II for every mission as well as standard heavies out of T1 launchers (I think I finally looted enough Malkuths to have an entire set to group now).

And yeah, I'm past the point where lvl 3's are too easy, and my skills are far from a focused build. So you certainly don't need to spend that long in BC's if you want to go to BS hulls.

This is what I use for L3s and I never, ever have a problem. I rarely get down to 50% shields unless I'm just messing around.

Adjust down to what you can fit but this will serve you extremely well. I use rat-specific T2 light drones sometimes but mostly Hobgoblin IIs. I use the light missiles for frigs and drones when necessary. Sometimes I swap out the missiles for a neut. I put the guns into two groups of three and stagger their cycle times. It is rare for ships to get close to me when using the AB to keep range.

I also need a PG4 implant to fit this, but it's worth it. Replacing a SPR II for a PDU II will work as well but you lose some tank.

Tanks 160 DPS against Angels, IF they even get in range...

[Hurricane, ArtiCane]

6x 720mm Howitzer Artillery II (Phased Plasma M) - 20k/32.9k + 329 DPS
2x 'Arbalest' Assault Missile Launcher (Bloodclaw Light Missile) - 20.5k + 19.97 DPS

10MN Afterburner II
2x Invulnerability Field II
Large Shield Extender II

2x Tracking Enhancer II
2x Gyrostabilizer II
2x Shield Power Relay II

Medium Ancillary Current Router I
2x Medium Core Defence Field Purger I

5x Hobgoblin II - 66 DPS