Which words should he write?
Radak: It is what Hashem will say now.
Why did Hashem tell him to write this Nevu'ah?
Radak: It is a consolation for Yisrael of that generation. Just like they will see the punishment soon, they will know that the great consolation will be at the end of days.
Malbim: Hashem did not send him to tell this to the people. Rather, He informed him, and commanded him to write it for a memorial for the final generation, for a consolation. Just like the dire predictions will be fulfilled, also the good predictions will be fulfilled.
Why does it say "El Sefer"?
Radak: This is like Al Sefer. Also "v'El ha'Aron Titen Es ha'Edus" (Shemos 25:21) is like uva'Aron.