The BizTalk Project from Hell

I took a permanent position with a consulting firm in November. They brought me on board to help them with a BizTalk 2009 project for a Healthcare project they started over a year ago.
Apparently they didn’t hire a qualified BizTalk Developer or Contractor. They decided that they would do the Application themselves.
They figured out how to create Orchestrations and how to use the BRE. Everything else was done in both Serialized and Non-Serialized .Net Classes. They called these classes from Expressions and Message Assign Shapes in Atomic Scopes.