1) I don't think so.For me the characters appear to be the same.
There are some different details,like in Movie 12 they say that Conan has perfect pitch and they don't do that in the manga but even that might be possible:
In the episode 385 Conan has an argument with Ran about the notes of Anokata's number.
In the episode 387 we can see that Conan was right although Ran is more musical (singing,playing piano).
Haga tells Conan that he got "good ears".It's not that easy to define the notes even if you're not musical.
So there's a good chance that Conan really has perfect pitch.
For me the movies/OVAs/fillers are well-made and they don't disturb the manga/regular episodes.
Of course,it's difficult to convert a manga to an anime.But comparing to other animes it's really close to the manga which I really like.
Sometimes filler appear to play in another month or something like that but the time line in Detective Conan is anyway really complicated.
2)Volume 48,Chapter 11 - Shinichi's birthday is mentioned.
3)Surely,Gosho does not make the entire movie but he has a big influence on it.
It seems like he is "overseeing" the whole production.
In 2011 in an interview he said that he is proud of movie 5 and he spoke about suggestions he made
for movie 15,drawing Shinichi's face for a scene and giving Conan a phrase from the manga that he liked.
So you see he is involved in the process.
Besides I don't think that they can make Ran blonde, Akemi alive or change detective agency just because they want it.
But how you write it seems like the movies would be totally apart in a different world but for me it's not the case.
I know that movies are in way separate ,plus I always wrote "For me" or "IMO" they are an extension to the canon.