Chances are if she went broody you probably won't find her. If it turns out to be the other extreme, I'm so sorry. I know how hard it is to lose your first one.
I have that in my other light beaked birds but I don't raise leghorns so I don't know. I'd say it's normal but I'm not positive. The RIR's develop slower so I would say that it would only be a sign of a rooster if the combs on one of the same breed appears larger than the others in that breed.
First of all, welcome! You have come to the right place!
Now as to your questions:
1. No, especially if you have a small number. You can use mix the straw (or whatever bedding you choose to use as long as it is biodegradable) and manure as a base for a compost pile if you like. Or perhaps you...
Everybody's flock molts, some breeds like longtails it's only once in a blue moon but they all molt. Sometimes you don't notice it because they do the process over time though. The best "medicine" that I know of. would be to separate the two that are getting pecked and keep them separate until...
It's hard and next to impossible. The easiest method is prevention in the first place. I will occasionally charge at a rooster or hold him down for a minuet or so to re-establish who's boss. The person the roo is attacking has to be the one to cure him and establish his place in the pecking...