Akira Uehara is feminine and sensitive, while Nanako Momoi is violent, chaotic and manly; but he has a crush on her anyways. One day Uehara is sent to Momoi's house to bring her some missed homework, and thus his life changes forever. For Momoi's grandfather needs someone to test out on his new invention, and since Uehara has arrived, he decides to use him instead of Momoi! However, by accident, Momoi's grandfather activates the machine when both teens are still inside. No one is hurt, but there's one unfortunate side effect: they've switched bodies!
Although how they become girls in these two series is not entirely the same, both series deals heavily between the relationship between the main male characters and their close childhood friend. Both series are quality reads, and especially recommended for those into the body swapping gender bender genre.
If body swap themed gender bender is your thing then Your & My Secret and Yamada-kun to 7-nin no Majo are what you are looking for. Somehow those two series are quite similar (although only Your & My Secret has the gender role reversal going on).
P.S. Keep in mind that Your & My Secret get's a bit confusing (and disturbing for some) with who is dating who...