Hi Skig,
Thanks for that, although it seems that it varies between disciplines etc. I've just had a look at the guidelines of the journals I'm approaching, and both say as an author I retain the rights to 'reuse' the article in a thesis, in whatever format I want. So it's covered from that angle.
Also, my uni stipulates nothing about self-plagiarism, although the general view seems to be that as long as I acknowledge that 'some parts of this thesis have been published in bla bla bla' then it should be fine, but I'll double check this anyway. Very confusing!