I'm in a big hurry and need some quick pointers on some basic Prince2 issues

1. How can I easily set up a risk log in Clarizen? How do people tend to do this?

In v6 Add Related Cases> New Risk. 

You'll see the Risk linked against the project on the Project Details page. 

You can extract a Risk Register report. A risk register is a risk log. 

2. How can I extract a Product Breakdown Structure or Work Breakdown Structure from Clarizen?

The Work Plan is the WBS. Select the top line, click on Utilities >  Export 

1. How do I create the Product Flow Diagram in Clarizen?

Clarizen doesn't have this feature. 

1. How do I record tolerances in Clarizen?

You can create a custom field to describe them.

There are a number of cost and revenue performance indicators you can use as inputs to judge your performance against the tolerance limits.

1. How do I set up an Issues Register in Clarizen?

There's a report: All Cases to be resolved in a specific project. 

I have some other methods to display Issue and Risks on a project level, but it requires some custom reference to object fields with reverse references and setting up layouts accordingly, which will be tricky to explain on a forum post. 

Thank you! That was quick!