Hi Jason, welcome to FISD
Looking at the photo (by the way you can use the Direct link option to post the image directly ,no as a link, into the post.), it looks like your armor is a RS prop master one.
1. To connect the shoulder to the bicep, should I just use more elastic fabric and E6000?
Yes, you can just glue the elastic if you have sized it correctly . You could use some snaps to allow making modifications to the elastic if needed (bellow a diagram and some images)
2. The shoulders are slightly different, does it matter which one goes on which side? Doesn't really seem like there is a pattern.
As a ruler of thumbs, in an accurate armor kit, the one with the the swoop at the bottom like that should be worn on the left/hand shoulder.
3. How far up does the bicep need to go into the shoulder?
It would depend on how they fit on your arms but it's supposed to let you move your arm to hold your weapon