I don't understand the third sentence: it's worth bearing in mind? What is the ей referring to?
Try to learn some basics of Russian grammar (An On-line Russian Reference Grammar is a good site for that, and also for going somewhat deeper) . One of the features is usage of Dative case (roughly meaning "to her") when using certain verbs or impersonal constructions in general, as in these cases a "logical" English subject may become an indirect "beneficiary" of action.
"Ей стоит" means "she should", so "ей стоит иметь в виду .." is "she should bear in mind".

Also, why is it not только, только нет мне нет слова в ответ? Does ни simply function as another нет, but changed for variety?
Yeah, like that though they are not interchangeable. "Ни" is a particle used here in one of its main functions. Namely, "not a.."/"not a single..." in negative sentences (compare "нет ни слова", "нет ничего", "ни слова не сказал").
You can also see it in neither..nor constructions ("ни слова, ни звука" - they also allow for neiter..nor..nor..nor, which is not exactly good use in English) and some others you will eventually learn.