Shinji's portrayal was one of the high points of the movie for me! The flashbacks early on (it covers about a year and a half before the war) really call attention to how much Shinji hates everyone around him (and himself), and shows how he and Shirou slowly drifted apart. There's even a part later where Taiga flips through a scrapbook of Shirou's childhood; the first few pages of pictures show him spending time with Shinji but once Sakura starts appearing in the photos Shinji's nowhere to be found.
2.Hassan used Kuzuki as a hostage against Medea, and then throws a knife in his face after killing her.
The Lancer/Assassin fight also happens shortly after Caster gets killed and her corpse stolen.
Oh, and as for the attack on the Ryuudou temple, the way the movie portrays it is: Bugs flood Shirou's room, Zouken manifests, Hassan appears outside Shirou's room, Saber attacks Hassan while Shirou attempts to fight of Zouken's bugs (Zouken's clearly just toying with him), the Shadow appears and starts attacking Saber alongside Hassan, Saber gets consumed offscreen by the Shadow, Hassan goes to find Shirou and starts to beat the crap out of him, Rider shows up and saves Shirou in the nick of time, and Rider fights off Hassan.