My 4 stroke 18hp cables came detatched from the battery while running and I assume this blew the charging capabillity. Anyone know of a process for diagnosis and repair?
Year is no matter; Model is everything. Likewise you didn't mention whether it's a Tiller (EF type) or Remote (EP type). I assume you have an NSF18B2. Why do you assume you aren't charging? Does the motor start with the electric starter? If so, you are probably OK. Running with the cables disconnected is OK; However shorting them while running will blow the 20-amp fuse.
The electric starter works fine. I will check to see voltage coming off the engine first and if not, will go a bit further. Is checking the rectifier fairly straight forward?
Yes. Full info is in your Factory service manual, available from any dealer, including me. Most common part to get fried if the wires shorted would be the rectifier, which is a garden-variety 4-diode bridge in marine-grade housing.