In terms of the F-27, since a box launcher can only be reloaded at a hanger deck or maintenance facility isn't it better to put the magazines on the carrier and have none on the fighter.
The only magazines on it at this time are those from the launchers themselves. (Basically, loaded missiles are treated exactly the same as ones in magazines as far as aurora is concerned. )
Edit:
And because I don't really like double posting, here's my thoughts on the OP.
. . . Snip. . .
Other notes (Writing these as I see stuff, so apologies about fragmented thoughts):
Long Island: Listed as carrying 1 Cobra-S, but no ammo for it. Also, I'd personally run with 2 sensor boats just for a bit of redundancy.
Raptor: will need escorts against any missile ship that's not been disabled. 8m is well within mid-tier AMM sensors, so it's almost certain to come under fire before it can offload.
And now I see that your sensor and FC don't agree, which isn't too bad considering the lack of ECCM but personally I'd still push out to the 24m from the FC as that's outside of most AMM ranges. Unless you're using them to take the beating of AMMs so that your missiles are more likely to hit, which I'm really not sure which way the efficiency goes. (Mostly depends on death rate for these)
Finally noticed the Gauss guns. Not sure exactly what I think about it, but it definitely would help with getting the missiles past initial AMM fire. Although, with that BFC you're likely looking at ~4% hit rate against your own missiles.
ASM Starfire: size 3,99? 0,01 Fuel will still give some effect, but I can understand it if the AGI modifiers work better at 3,99. (Numbers like that just bug me >_>)
F-27 Anaconda: just looks plain odd to me. For anti-fighter work you really don't need the extra FCs. For AMM work you'd want it to be faster so you could get better chances against missiles speeds. Also, the weapon type split is definitely resulting in inefficiencies, what with the need for 2 different types of FC and the differing combat endurances.
Also, the F-27 is in fact, less armoured than the F-28s.
Okay, just noticed that the Carrier for this carries the AFMs. That makes it a bit more interesting. While all of what I said stands for what's on the BP, with the AFMs it's a reasonable dual role ship, if a bit lacking in kill vs Fighters (2 internal damage in worst case vs 2 layers of armour) and a bit lacking in range vs Larger ships.
Oh, and I'd love to see what the mass of extra missiles does to some other parts of the code.
F-28 L: If you're looking for an anti-ship fighter, this would be great. Not so good for anti-fighter work. The FC is letting you use less than 1/2 your possible tracking, which means that any fighters at equal tech are going to be really hard to hit. 1/5 of the fighter is engine, which personally I tend towards 2/5 to 1/2 (resulting in speeds of ~96000+km/s, well outside of what your fighter could deal with. [Napkin math, not in-game tested])
The FC is also limiting the range on your laser meaning that it's going to end up within range of most Meson ships of FAC or larger. (Meson fighters might be another matter, but I can't remember any example ranges for them at this time)
F-28 M: FC and Sensor don't agree on Resolution. Anything of fighter size (<=10 TCS) will not be seen by the sensor until ~80,000km. Missile speed could also be an issue (see my napkin math for fighter speeds above).
Otherwise, good call on the multi FCs. Although, I might've tried 3 with only 18 launchers. ~18 effective damage per target, with fighters likely to be 1 to 2 layers of armour (4 on really heavy ones) this means ~8 internal damage against 2 layered targets. (0 for worst case against 4 layers, but with a bit of luck you're still likely to cause a lot of damage) [My personal targeting at this point would be using 2 of the FCs and leaving the third for mop-up. Which means that the third in unnecessary. Huh. ]
Carriers:
If these are likely to be working in groups instead of solo, I'd personally switch out the CWIS for turreted AMS systems. The loss in size efficiency should be more than made up for being able to bring the entire carrier group's AMS to bear on each barrage.
Final notes:
Oh, you massively out tech everything you're fighting. Okay, so most of my notes about speed aren't terribly relevant, but I'm now very surprised you left the 80k km range on the Laser. (Which probably needs a better name, I wouldn't use a 6 damage laser for anti missile work. )
And, in-case you don't have something already, a scout FAC with the best cloaking and thermal reduction you can manage is huge for being able to engage on your terms.