This is an excellent recent account of organising and completing a transit on yacht Brio.

Achieving anything in Panama can be frustrating, but as this website and this article demonstrates it is entirely possible to arrange a transit through the Panama Canal yourself, rather than employing an agent.

As with anything this major, it is when things go wrong (and they do!) that you might appreciate the assistance of an agent, not least due to the language barrier, but also just with the difficulty of dealing with such a large organisation.