PRE-INFUSION: 
 
In addition to the six fundamentals of brewing, there is also the matter of pre-infusion. It is important to realize how pre-infusion affects the final product in manual brewing.

 
Pre-infusion gives you control over clarity and extraction of the coffee brewing process. The purpose is to allow the cell surfaces to be saturated. The goal of this is to remove the material that is bound up in the cells of the ground coffee by controlling the initial volume to completely saturate the material, allowing time for absorption with little extraction. Once all of the coffee has been saturated each grind particle, assuming that it is the same size, will then extract at the same rate, creating a more consistent and even brew extraction.
 
As a general rule of thumb, pre-infusion should last between 30 seconds to 1 minute and the amount of water used should be about double the mass of the dose of coffee used to brew.
 
EXTRACTION AND BREWING:

Two factors that effect brewing are Extraction and Percolation.  Here is a little bit more info on the likes of these:

Extraction involves a separation process consisting of the separation of a substance from a matrix or sample.

Percolation (from Lat. percōlāre, to filter or trickle through) concerns the movement and filtering of fluids through porous materials.

Brewing coffee is the process of extracting the soluble and some insoluble components of ground coffee into an aqueous solution. Brewed coffee is the result of strength (soluble concentration-ie.coffee mass) and extraction (soluble yield or mass suspended in liquid). Brewed coffee is around 98.8% water combined with 1.5% coffee flavor particles.
 
There are several factors that will affect the extraction, namely: coffee/water ratio, grind particle size, contact time, coffee bed depth, amount of turbulence and water temperature. Understanding how each of these factors is interrelated to the final product can help troubleshoot and fine tune the brewing process.

Pour-over brewing and Chemex methods are a combination of Extraction and Percolation. As with brewing espresso, the recipes should have an ideal time and volume. In order to achieve this, the grind particle size should get larger with the more volume one brews. The grind should be coarser while brewing 24oz of coffee as opposed to brewing 12oz of coffee. In this example there will be more coffee mass for the fluid to percolate through, so to achieve the proper extraction time, the grind particle size needs to be larger to increase the flow rate.