A couple years ago I was reading a lot of manga and there is one title I'd like to revisit.

I can't remember everything about it but I do remember that the female lead starts off as the unpopular, bookish type. She lives with her grandmother until she suddenly passes away. (This occurs in the first chapter, I think.) Then the male lead gives her a makeover and his family takes her in. ALSO, point-of-interest, I remember that there was something about them being "flowers"? They had pheromones, or something.

If anyone can tell me what this is, I'd really appreciate it. Thanks!

I believe you're looking for Hana ni Nare!.

Wow, that was quick and you are correct!
Thank you so much!