I will be writing my dissertation on these two conflicts, focusing primarily on the similarities and differences in the counter-insurgency methods used. I was hoping for some suggestions as my university's library is somewhat lacking. Thanks in advance.
Not an expert on either, but have you come across Learning to Eat Soup with a Knife by John Nagl? It's precisely a comparison of these two conflicts.
CSI Research Survey 6: A Historical Perspective on Light Infantry Is a comparative study of military tactics used by light infantry. It has an interesting chapter on British tactics used in the Maylay Emergency and the Konfrontasi. It is also available for free as a .pdf Here