Hi Steve!
I usually size my chains by placing the chain on the big-big combination (cog and chainring), then pull the chain ends to meet, then add two links before cutting (per Shimano's instructions). This ensures the chain will be long enough in the most demanding state while being minimal in length to keep chain tension reasonably high to prevent chain slap in the (largely avoided) little-little combination.
Keep in mind, extreme cross-chaining (i.e. big-big and little-little combinations) leads to rough running and greatly increased drivetrain wear thanks to the extreme angles involved, so best avoided in actual use. With most 9-sp transmissions, the secret to long life is to use cogs 1-5 with the small chainring, cogs 3-7 with the middle chainring, and cogs 5-9 with the large chainring to minimize chain deflection.
You'll also want to make sure your B-tension screw is adjusted properly so the upper jockey pulley will clear the large cog in the big-big combo, yet not be so far away as to adversely affect shifting. I generally go for about a 5mm-6mm gap (also per Shimano's instructions).
Looking at your photo, I would suggest shortening the last bit of cable housing as it goes into the derailleur. You should be able to get a straighter shot at it. Big score, lovely bike!
As for chainstay protectors, I ordered an M:Part carbon chainstay protector to go with my 2011 Sherpa. It attached with adhesive on the back as well as a couple cable-ties. It held very securely and did a nice job protecting the 'stay. I am sad to see it no longer appears to be in SJS Cycles' current inventory. Some of my other bikes have adhesive-backed stainless chainstay protectors. While other people are happy with "LizardSkinz" style neoprene sleeves, I tend to avoid them because I have found they can trap moisture and even grit beneath, causing problems over time. I've also used clear plastic protector tape, but found it can become pitted and looks pad over time with continued chain slap.
Finally, I've found Shimano's "Shadow" series of rear derailleurs are more resistant to chainstay slap because the upper pivot is fixed, rather than spring-loaded.
Best,
Dan.