Interesting work, Tweaky. I also had some small issues with veneer lifting at the edge of the neck cavity, but stuck it down with some watered-down PVA and now it's fine, plus it's all covered under a very dark tobacco finish. My neck joint fit is a lot better than yours, not 100% gap-free but any gaps are very small indeed and if the glue doesn't fill them, then filler will.

I bought some thin CA glue after watching a StewMac video on drop-filling small chips in the finish (I just used eBay to find some). Boy, that stuff has a very low viscosity and surface tension. It gets everywhere! If you want it to run under an edge (like a lifted ply laminate) it will do - but it will also run everywhere else at the same time. You really need one of those very long thin adapter nozzles for the bottle, as the standard nozzle just has too large a hole to regulate the flow and it's easy to get it everywhere.

Otherwise I haven't knowingly used any medium CA, just the standard domestic CA tubes.

Hopefully the weather should be improving for you by now, so that you can at least work on the guitar outside.