That bike is gonna be awesome!
I had an idea about the upper shock linkage. The Kawasaki ZR6 shock uses an upper link (in the later models), and perhaps you could fabricate and adapt a similar link to your Honda, rather than welding on a new mount.
Picture the link in the attached picture turned 90 degrees towards the existing mount. Maybe you could make something similar that allows you to simply bolt in. You'd need to secure your fabricated link in two places, so it wouldn't move. The stock bolt location is one, and then perhaps you could drill another hole for a second bolt.
