More school stuff (boring, I know)

In terms of degree requirements, I've got my ducks in a row. Now I'm just waiting for the results of my petitions to remove the Mystery Grades, and I'll be ready to start thinking about grad school.

Question! I'm currently retaking a class I dropped too late to avoid receiving a bad mark. Pretty sure the new grade will be an A, and in keeping with school policy, will override the original mark. Should I apply to grad school before or after I've finished the class and my transcript is updated?

Complicating things, I have a failing grade on my transcript, also from dropping too late (during the year of madness), that I can't get removed or overridden. It drags down my GPA but even with it, I'm in the B+ - A. Assuming I do well this year, it gets closer to the A range, and just one A+ would put me solidly in the As. Looking at the senior classes individually, I've got one B, one E and some As and A+s. I'm not worried about my abilities to keep up that trend this year. I think it should be fairly clear that the E is an aberration in an otherwise good transcript.

Anyone with some insight into the grad school applications process, with some advice for me?

* Yes, I am booking official advising appointments as well.

ETA: I forgot the thing that originally made me want to update. The department of Women's Studies sent me a letter suggesting that I change my major (at this late date?!), declare a minor, or just take more Women's Studies classes. Is this something departments commonly do? It seems kind of a bizarre recruitment move. I mean, poaching?