I like to be really careful with my grammar so I think I can help:
1. The first option, because you use an observation, and not really a descriptor.
2. Again the first; she doesn't blink the words, therefore comma not really appropriate. Period also allows the pause that a "blink" usually insists.
3. This depends on the emphasis you want:
a)If "Bugger" is the yell, (as implied by first option) could just use an exclamation point. ("'Bugger! If I have to...'"
b) If the "If I have to..." is the yelled part, same option with ! ("'Bugger. If I have to...!'" Exclamation marks are more readable that "she yelled" as the reader can easily figure out the tone by surrounding situation and such punctuation. Or, another approach is to extend the descriptor, turning "she yelled" into: "she raised her voice so X could not ignore her,'If I have to...'")
c) If, however, everything is yelled, don't use a period - just extend the sentence:
" 'Bugger!' Alleyah yelled, 'If I have to...!"
(notice that the exclamation mark has a different effect on capitalisation compared to a period, like
"'Yes!' he yelled." rather than
"'Yes.' He yelled." and it also affects the way it is read - depends on what you want to get across.)
I SO hope that I haven't confused you more! *My Penguin writing/grammar book is my best friend...*
I've read in articles that "yelled" is not a popular option - it's very vague and doesn't get the desired effect with readers. Alternatives are "shouted" or "cursed" or "screamed" or "erupted" or "bawled"....etc.
Cheers! (And best of luck with editing...my least favourite part.)