Hey Mike --
You've been busy!
Would be good to see more of the ziva side of your setup. It would be easier for me to get a feel for your system if I could see:
How big the tets of your tissues are
How many attachments overall you're using
What fibers if any you're using
As for best practice with attachments. A good rule is to use small attachments at the origin / insertion points at the ends of your muscles. By small attachments I mean small groups of vertices. Do a broad strokes setup where you only do origin / insertions.
Play back the scene with some basic animation on the character -- maybe he's going through some basic shoulder poses or something. From there you'll be able to see how your muscles are performing and gauge what you need to do from there.
In general with attachments, you want to be as sparing as possible. Using too many attachments will result in your system being over constrained and won't give you the nice organic results you want.
Use fixed attachments to attach muscles to bones at origin/insertions. Use sliding between muscles or between muscles and bone when you want to preserve the distance between bodies but allow them to slide tangentially.
Looking forward to seeing more!