Probably in 2005 the design of a complete assembly line is a $100 million project and the actual implementation in the range of $1 billion.
Similar costs are reasonable expectations for a mechanosythesis effort.
Some current protein design work:
David Baker, who's team created Top7, the first articial protein in 2003. They are developing improved methods to predict and redesign protein-DNA interaction specificity, and extending their protein design methodology to the design of enzymes that catalyze chemical reactions not catalyzed by naturally occurring proteins.
A discussion of possibilites for creating artificial enzymes These are generally synthetic polymers or oligomers with enzyme-like activities, often called synzymes.