Make sure you are deleting one side using Face Mode, not by vertices or edges.
To add faces to something, you can use a variety of tools. Fill Hole, Append to Polygon, Bridge.
To combine your shape with another shape, just select the two objects and go to Mesh > Combine (then delete your construction history). This will force the model's vertex order to reset and might help with deleting those floating polygons.
Thanks guys. I may have figured out the issue myself. The model was originally in ZBrush, and I exported it again without polygroups. Thanks for the other help though.
Replies
To add faces to something, you can use a variety of tools. Fill Hole, Append to Polygon, Bridge.
To combine your shape with another shape, just select the two objects and go to Mesh > Combine (then delete your construction history). This will force the model's vertex order to reset and might help with deleting those floating polygons.