Eric,
Many of your questions I could not answer without seeing the project; however, I would offer the following input.
While photos are not real good for someone else to assess many things, the photos of the fuselage covering are sufficient, in my opinion, to think that the fuselage should be stripped and recovered. The misc damage, poor finishing and questions you have about what process was used in parts of the finishing would cause me to want to strip it and start over. Also, while it is an esthetic thing, the finishing of the shape of the end of the VS isn't too pretty and that cannot be fixed unless the fabric is removed - pretty easy to do with the fabric off.
I cannot see enough of the wings in the photo to venture a guess on them.
Since you mentioned you are not familiar with fabric covering but are considering building a fabric covered aircraft, by all means - get the Poly fiber book titled "How to cover an aircraft" if you are going to use their system. Really straight forward, practical and would solve a ton of questions you have and it is essential to using their products.
On the lack of documentation, I would go to, call up, the horse's mouth (your faa MIDO {Manufacturing Inspection District Office}) and ask them since they are to ones having the final call on the airworthiness of the aircraft anyway. I found our office very helpful and they do have work arounds for unique situations.
I have three friends who built S5s and they all really, really like them.