Are there not pre-made stantions of metal (brass, et al) that are pre-drilled for railings or cables? I've seen some on a build somewhere. I'd bet they're available in various sizes/scales.
http://www.harbormodels.com/site08/stanchions.html
Also, is it possible to mount the stantions just inboard of the gunwales and affixed to holes in the main deck level? Then they can also be CA'ed to the gunwale itself. Might not be scale or proper but they would be reinforced.
I have the kit too and the method you're using is precisely the one I would have picked. Tedious indeed but then the reward, the personal gratification is always in mind...