a
with
They cannot be translated in this context. There are no articles in Russian and we use know no prepositions "to denote an instrument that helps to make something," we have the special form of a noun for it (the prepositional case). So, "карандаш" means "a/the pencil," but "карандашом" should be translated "with a pencil" in this context.
Я - I
пишу - write/am writing (depends on the context, there is only one present tense in Russian, and this form is used only for the first person, like "am writing", not like "write" in Present Simple - I write, we write, they write...)

But you don't have to look into all this, this chapter just represents the idea of cases in Russian for you to know what you'll have to deal with. (:
How do you eat an elephant? One bite at a time.
Everything is translated and explained there, I can't understand what you want, sorry. Words you need to pay attention to are in italics (both Russian and English ones).