Doubt that you've missed that much - look upon Act I as a trainer for the rest of the game - well the first half of Act I anyway - when things are looking grim try these pages again.
Killing Bryant does not alter the plot that much as you wil probably end up killing him anyway just for the XP

and the item you need is there all the time.
If you've sorted Samuel the first time round then you should have access to BF3 - when you have access to BF3 you have access to BFs 1, 2 and 3 - in other words all lower BF numbers. Hint: remember this for later in the game.
Not giving anymore spoilers (fresh out of them tonight) but as you have to go back to the earlier levels anyway consider turning lights off before a locked door - or is that on - or is it a combination of the two. The tooth fairy may be kind and give you a bonny doll.
Keep in there - its worth it.
marts