For the first, I think it was meant to look rushed; the Homunculi had been banking on Roy performing human transmutation in exchange for Riza's life, and seemed pretty set back by him refusing; Pride mentions that forcing him was a last resort, and it seems to take a chunk of Pride's stone or something to do. It was their final resort plan with the only sufficiently powerful alchemist to hand (I don't know if they ever acknowledged Scar as an alchemist; he has his brother's arm, but it's unclear if he ever actually studied alchemy for himself).
Didn't Ed use his own soul like a Philosopher's Stone? He used his soul as a Stone once before, when he healed himself. I think it's also partly to do with the fact that Ed and Pride are basically cousins. As a Stone, Ed was able to move in and out of Pride's Stone. Oh, and Kimblee wasn't helping Ed; he was being a dick to Pride. Much earlier on, he commented that he was genuinely looking forward to seeing which species would win the fight for dominance, Homunculi or humans. He got annoyed when Pride chose to save his own life by possessing Edward, something that Pride had already jeered at Greed for doing. Kimblee got annoyed and decided to be a dick for the hell of it, which has been his MO before.
I think because Hohenheim took the time to calm and talk to his souls, and help them regain their own conciousnesses, they became capable of using their own power independently. He planted them at the points of the circle that would reverse the creation of the Amestrian Philosopher's Stone, and when the shadow of the sun moved into the right place they activated themselves. Without that 50million strong stone, Father didn't have the power to restrain God and fight at the same time, so his Xerxesian stone was massively strained. I think Hohenheim's stone was able to act independently at other times, too.
Wasn't the Gate something Ed began to realize after that time in Gluttony's stomach when he transmuted himself, and saw Al's gate? He realized that their bodies and souls had become connected at that time (he then went on theorizing that the reason that he's short is that his own growth is being divided equally between his body and Al's, and that was also the reason that he slept and ate so much). He might have already came up with the idea that the Gate could be sacrificed, but the problem is that the Gate is the only way out of that place, so sacrificing your Gate would normally trap you there. He could only do it because he and Al were connected, so he could leave through Al's gate. Anybody else sacrificing their Gate would be trapped forever.
