As mentioned by OP himself, the Blu-Ray version has some extras , including Goro Miyazaki, the director, talks about the differences between the manga and the movie.
Director Goro Miyazaki on Yokohama – (15 mins) Miyazaki talks about making From Up on Poppy Hill a period film and the differences between the manga and the animated film adaptation.
Director Goro Miyazaki on Yokohama (18 min.; HD): From Up on Poppy Hill's director speaks about shifting the original manga's setting to 1963 Yokohama, striking a balance between authenticity and properly cinematic visuals, the history and geography of Yokohama, and even a few notes about ideas that didn't make it into the finished film. This is a conversation that would benefit from some tightening in the editing room but is still well worth taking the time to watch.
But for the starter, Japanese Wikipedia lists some of the major differences:
The movie followed the original manga's theme and setting for main characters, but the plot and story presentation were greatly modified, making it an original work.
- The introduction of "Quartier Latin", the high school's newspaper club's clubhouse as the original material in the movie. Shun and Shirou were trying hard to protect their clubhouse which had been planned to be demolished. Umi, trying to tell the goodness of the clubhouse to the students, proposed a clean-up and become close to Shun through it. The movie's storyline was largely constructed around this "building conservation" act.
- The timeline in the movie is around May-June 1963. To prevent extending the school year, Shun was placed in 3rd year from the beginning, Umi's 2nd year, and Sora's 1st year.
- The school uniform was changed from blazer to sailor suit.
- The main character's surname was changed from Komatsuzaki to Matsuzaki.
- The lodger Kitami Hokuto's name was changed to Miki Hokuto, the gender from man to woman, and the profession from veterinarian to doctor.
- The main character's mother Nijie Komatsuzaki's name was changed to Ryoko Matsuzaki, the profession from cameraman to college's associate professor (English literature).
- The setting about mahjong gambling was cut.
- Regarding the suspicion about the birth, it's revealed that the photo of father that Umi shown is the same as the photo that Shun had.
- Umi's grandfather, Shimatarou is no longer alive, and many characters in the manga didn't appear.