Heat shrink along the gear cable down to the BB would be neat, as mentioned.
As for the mudguard, SKS do a kit for this but of course there is no way of knowing if the clips will work on your guards, and you don’t need the wire, but it shows that they think some kind of protection is a good idea inside the guard:
From front light to bike, you can do this to create a coil to allow for movement, tends to stay in shape fairly well:
https://www.flickr.com/photos/lovely_bicycle/6297144534/
You can get coloured zip ties so you’d be able to get something less conspicuous than plain black for the down tube, as in some bits of this:
http://lovelybike.blogspot.com/2011/11/aftermarket-dynamo-lights-clean-look.html
Heat shrink along the gear cable down to the BB would be neat, as mentioned.
As for the mudguard, SKS do a kit for this but of course there is no way of knowing if the clips will work on your guards, and you don’t need the wire, but it shows that they think some kind of protection is a good idea inside the guard:
https://www.bikester.co.uk/sks-cable-routing-kit-M172682.html?vgid=G8515&cgid=37004#&gid=null&pid=1
I used this stuff for part of my dynamo wire run - wire just about pulled through it with a bit of soapy water:
https://www.amazon.co.uk/gp/product/B001BPRZP6/ref=ppx_yo_dt_b_search_asin_image?ie=UTF8&psc=1
PM me if you want some