For #2 there's a story called Semper Fi at FanFiction.Net written by San Antonio Rose. Sam gets a call telling him that Dean was wounded by an IED while serving in the Marines in Iraq. He and Jess go to the hospital in Germany to take care of him and bring him home. Due to a demon attack (since Jess wasn't in the apartment to be put on the ceiling) Dean loses a hand. With the help of his brother, sister-in-law, and his new friend Cas (and later, his father) Dean has to deal with his recovery and get used to living as an amputee, while still knowing the yellow eyed demon is still after his family. There are also two missing scenes in a separate spot in the list of the author's stories which I didn't see on the author's lj page -- sarosefics.livejournal.com -- dated October 7, 2010 and tagged marine!dean. Or through ramblin_rosie.livejournal.com; same date.

I also have to say this isn't the only good story by this author. Hope you enjoy 'em.