There's another current thread discussing priming on the sprue that might be somewhat relevant:
http://www.dakkadakka.com/dakkaforum/posts/list/668042.page Regarding the glue, I'll just copy/paste what I wrote in the other thread:
Plastic glue will bond the paint, just not as well as if it were a plastic to plastic bond (it will slightly melt the paint). Superglue doesn't bond the paint well at all (as it only bonds to the surface of the paint).
However I usually clean a bit of the paint off before gluing together either way. The area doesn't need to be perfectly clean, I usually just scratch a bit of paint off with my knife.
As for priming before or after assembly, I usually just assemble as much is practical before I start obscuring things I want to be able to paint later. It's a judgement call, there's no black and white of "always assemble before prime" or "always prime before assemble".
I'm not too concerned if the primer doesn't fully coat some of the hidden areas, those areas only typically need a very light dusting of primer anyway. It can act a bit like zenithal highlighting anyway. What concerns me more is when it comes to actually painting the models whether or not I will be able to reach the detail, if I don't think I will then I build sub-assemblies rather than assembling the whole thing before priming and painting.