I think Shaun's post assumes way too much knowledge, especially for someone describing himself as a "newbie." I will attempt to explain things so Shaun's post can be better understood. (Shaun, jump in if you disagree with something.)
In the Japanese language, most nouns (especially complex ideas) are represented by written characters imported from China. Kotodama is usually written with two Chinese characters meaning word (koto,) and soul (dama.)
To put it very simply, people who practice kotodama, chant certain words to bring about specific results. It is similar to (exactly the same as?) saying, "Abracadabra" in western forms of magic.
Now to fully understand Shaun's post, it is important to know that some people (most famously, Morihei Ueshiba) believe that the indigenous Japanese language (before the influence of Chinese) is an uncorrupted, pure language handed down by the gods. Shaun lists differing words that share similar sounds. To the average Japanese, there is no connection between them. As they are schooled thoroughly in the Chinese characters, there is no confusion between, for example, ball and bullet, even though they are pronounced them same as Shaun points out. This is because, in my opinion, the Chinese characters are different.
To those who study kotodama, there IS a connection between words that sound the same. The connection and the meaning, however, are not revealed without a great amount of study, reflection, and hopefully direct guidance from a teacher.
This is what Shaun means (I think) when he writes about translating "Yamato no kotoba" (the uncorrupted form of Japanese) into Japanese (the now common Chinese influenced Japanese.)
Bryan, I personally highly recommend John Stevens' books on Aikido, especially The Secrets of Aikido. (Shaun, is this what you mean by "public sources?) It is very clear that kotodama was very important to Morihei Ueshiba, and even if you go no further than reading about it, your understanding of Aikido will improve.