AFAIK, it's not possible to change chance of breach/fire system/crew damage depending on how many layers of shield beam (any weapon, particularly) passed.
Also, I don't want to sound rude so don't take it wrong way or anything, but I think it's good idea to play a longer while with the mod and overall, stick around discussions here, before proposing weapon/mechanic changes (unless you're absolutely sure, that you got struck by genius idea

). For example, the weapon type you're proposing is basically applied already, as much as it's possible to mod it into game - as said, via focus beams.
It's not related to adaptive beams in any way, BTW - it was in CE way before AE (of course, nothing prevent to mix it's mechanic with adaptives, creating adaptive focus beams - I vaguely remember seeing those too in game already, I think). It hits one room, can't miss, and have damage reduced depending on how many shield it passed - without draining those shield bubbles. Nothing prevent portraying focus beams as railguns, but I think that focus beams are quite established and polished in CE, so personally, I don't see particular reason for replacing it with something that only looks different (even if railguns/ballistic, non-explosive projectiles are quite fun idea, on itself - I tend to like those S-Fs where big dreadnoughts are firing at themselves with propelled mass weapons from caliber 100 cm guns rather than energy-based weapons, as it seems more appropriate for steel behemoths fighting themselves.)
Again, I don't want to sound discouraging or anything - it just a pity to see you "wasting" time on creating images for weapon that either can't be introduced into game, or is there already, under different form (unless Sleepy find a way to make use of those graphical ideas in other form, that is).
Also, when proposing changes of mechanic (not related to your post, but overall, about ideas that sometimes pop-up in this thread, from out of nowhere), it's very delicate matter. Let's take my humble example (sorry in advance

) - I'm here till quite early days of CE, and with all the amount of text that I produce here, I've proposed literally 3 changes to how certain weapons work gameplay wise. Just because is so FCKN delicate matter, and you need to really know this game in and out, test everything triple, etc - or your "awesome" proposal may, in fact, turn balance upside down. I'm amazed, seeing how effective Sleepy's mechanism for basing weapons at vanilla reference turned out to be in practice, with only few minor flops, corrected quickly, thanks to thoughtful input (and slow, careful approach to problem) from seasoned players.
The thing that after some time, just by reading, you get to know quite accurately what can and what can't be done via FTL modding, so you don't waste breath/worktime on outright impossible proposals. And that comes from someone like me, who haven't touched creating a smallest FTL mod, ever
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Micro bug report:
1. Lanius surrenders doesn't give Zoltan negotiating blue event:
http://s7.postimg.org/gny871q21/lanius_zoltan.jpg
Not sure if it's a bug or a feature (Laniuses being ignorant to Zoltan Authority), but I guess that even the sole talent for negotiating could give greenies an edge here. Same apply for negotiating a PLAYER surrender, BTW - blue option is lacking.
Suggestion: When we're at Zoltan surrenders - I'm not entirely sure if the possible outcome where we "drop down our shield and engines and take whole salvo on the hull" is really good idea. Usually, when player choose option saying in blue letters something like "Those people can be still reasoned with, there is no need for violence", lowering one's shield and letting enemy damage you without reaction isn't what comes to mind. While whole way of acting makes sense when facing Zoltan border police etc (we know that they moral codex won't allow them to shot on defenseless opponent), it isn't making much sense when fighting thieves, pirates, or desperate people in quarantine sector (aka - anyone that can still shot at us with high probability). Or at least, it could give further option, like "We lowered our shields and stopped engines, but they're still coming in at attack vector, weapons hot!" that allow to change our mind and fight anyway.
2.I remember that the wreckage field which could result in ABADOTH quest is AE thing, but I think that CE could fix it anyway:
If the outcome of searching the battlefield is encountering Mantis ship that just jumped to (probably) finish the job, we're getting loot *only* from that mantis ship, completely ignoring wreckages, that were said to be plenty and contain much scrap, just a screen earlier
Cheers,
/Estel