There does seem to be a cross over here, so merging in principle seems like a good idea..
Immediate thoughts:
This repo was originally geared towards Jekyll. It became apparent that this was more of a hinderance than a help, so I wouldn't want to put that emphasis on it again.
When you say "pick and choose" the CSS, do you mean there would be add-on stylesheets (much as we are starting to get here), or completely different 'themes' in a single repo? If I understand correctly, in jekyll-template the choice is currently Bootstrap v2 and Bootstrap v3. (I'm not convinced offering a legacy version of Bootstrap is worth the added confusion for users just wanting to get a site up. Why not just say "add this CSS and your done"?)
Does jekyll-template offer anything that this repo doesn't (aside from instructions, which are currently lacking), or would you say that one is duplicating the job of the other?
Merge with https://github.com/okfn/jekyll-template (?)
The idea would be to have a common set of layouts (and standard css) that we have in one place with one set of instructions.
Logic for together not separate would be common set of css that people could pick and choose with.