What are the pros and cons of using either site-directed mutagenesis protocols? I'm trying to find some primary sources on the topics too. Thanks!

You really don't need a kit for site directed mutagenesis. The basic principle in both is the same....amplication of the entire plasmid by a high fidelity polymerase with the mutagenic primers followed by digestion with dpn1 to remove the original template. The Q5 system does the ligation before transformation, whereas the quickchange relies on the bacteria's on ability to repair.

 

You could spend over $250 on a 10 rxn quickchange kit, or you could buy a high fidelity polymerase, like pfu ultra for ~$100 bucks (and much more than 10 rxns...good for other applications) and a tube of dpn1 for ~$60, also good for more than 10 rxns.