In general, good koji rice has all grains completely covered in koji, and the koji hyphae penetrate deep into the grain (it is the enzymes secreted by the hyphal tips (the ends of the mold cells) that lead to saccharification). The whole process takes about 48 hours, and for the final half of the time, the koji rice is cultivated in special cedar “boxes” seen in the above photo. In the box, the koji rice is about 8-10 cm in thickness, and is covered with several blankets to keep in the heat and moisture. The temperature is very important in the process and will dictate the quality of the koji. The koji spores are sprinkled on the rice when the rice temp is around 32-33C, and throughout the process, the temp gradually rises until approx 42-43C when the growth is complete.

- Information taken from http://thesakechronicles.wordpress.com/2010/01/17/koji-rice/

I reckon these could be some tips that I could use for the experiment.