If I had my way I'd combine Kraven's Last Hunt, the lead up to the marriage (i.e. cold feet) aspects of MJ and pete getting married from the marriage annual issue, the 30th anniversary Lizard story (for how to depict the good doctor as a monster and his goals, thus replacing Vermin from KLH) and ASM #44-45 (Lizard breaks Spidey's arm, Spidey in a sling for the climax of the movie and if there was a wedding at the end, Peter trying to hide it, a black eye, etc. for some nice Parker luck humor like in SM2).
BUT
As my idea for SM4 will likely never happen, all we know for sure it seems is BC is in the movie. I would not take from any particular story for that but rather adapt for the essence of her early appearances in the '80s as a comely thief/ally who is both seductress and untrustworthy, but not a through-and-through villain a la Catwoman. I'd also take a cue from SSM, the new cartoon, and not introduce Felicia Hardy, if at all, until near the end of the movie and keep BC as an anonymous presence for SM and not a new love in his life. I know Raimi likes connecting things to Peter, but like the video game that he helped guide, SM2, and the new show, less is more with this character and can add a new spin on a character as opposed to the clandestine origin in the first 10 minutes or the dippy reworked origin that was used for Elektra and a slew of other female characters in such a film. That I am opposed to.