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This is not "programming" related as much as it is "software engineering" related.

I am required to produce an implementation for additional functionality to a complete system. All I am armed with is knowledge of the existing architecture and a functional spec with visual requirements, user stories and use cases. Is there a standardised way to go about this? I suck at documentation.

A: 

Analyzing and designing a solution often follows a process a.k.a. methodology. The outcome of the steps are artifacts a.k.a. documents.

This related post indicates some free methodologies:

http://stackoverflow.com/questions/337708/rational-unified-process-alternative-for-documentation-and-templates

Jennifer Zouak