Well sorry to hear the end result for you msimonds

I hope you get refunded without to much issue.
Personally I would have smelt a rat if someone was quoting too little for a job such as a complete custom cms and I find $800 very low and a promise of completion and full 100% live tested inside 5-6 weeks as highly unlikely, but then I do not know how big this cms project was/is.
When paying in advance what ever the % you really need to be knowing in advance some kind of reputation of the person your intending on having undertake the task. Its not an unheard of practice for some advance payments as the shoe can be on the other foot just as much. The % you pay up front should be relative to the job size, the larger the job the smaller the % as extra topups of advances can be made as progression is made.