I had a meeting the other night with one of the new lecturers in EGS. He comes to UCT from the USA and seems to work days, nights and weekends. Our meeting started at 9pm (night owl that I am). I went over my last couple of months and where I see myself heading this year. I was offered some interesting advice.
Plan your thesis so that it fits into two or three papers plan what you want to present in the papers and then your research has a focus, a streamlined idea. Plan the figures you would want in a paper, no more than ten that summarise of highlight something you wish to discuss. Anything more you probably would just add to your thesis and never explain properly in the flow of text.
Think about the type of journal you are aiming for, is it a review of the literature available? Most journals want to print new work so if you want to discuss old work you have to include suggestions of new areas open to this type of technology or how the literature has lead to the experiments you're working on.
Do not go into a doctorate working for three papers and not a thesis. A thesis is a valuable tool to present a body of work as it developed. UCT has a newish option open for doctorate students, doctorate by papers. Your thesis is them a collection of three papers published and an introduction and conclusion to link them all together. The nice option is that if the papers are already published, the examiners cannot fail you, your work is already peer reviewed for every paper and they are more making constructive comments.
Plan your timetable to produce at least two papers by the middle of your second year, and a third by the end of the second year. This way you have time to write up your thesis and get published before you head off to post-doc and don't have time anymore.
Just some food for thought, use, don't use.