Andrew Zhu | Xhinker

Persistence Store and Instance Store actually indicate the same thing.
In WF3/3.5, the type is

   SqlWorkflowPersistenceService

So, people usually call it Persistence Store. while in WF4 the type is:

   SqlWorkflowInstanceStore

People call it Instance store.

There are other different conversions between WF3 and WF4. for example, in WF4 workflow service refer to persistence service and tracking things. while in WF4 workflow service refer to WCF workflow service. 

->"Can anybody provide the persistence architecture diagram for reference."
If you want to extend WF3 Persistence Store. please see:
http://msdn.microsoft.com/en-us/library/ms734700(v=VS.90).aspx
A sample:
http://msdn.microsoft.com/en-us/library/ms741725(v=VS.90).aspx

If you want to extend WF4 Instance Store, please see
http://msdn.microsoft.com/en-us/library/ee829481.aspx
Here is a xml instance store used in this sample:
http://msdn.microsoft.com/en-us/library/dd807514.aspx
I extracted the xml instance store, see:
http://xhinker.com/post/WF4Xml-persistence-store.aspx

Also post in:
http://social.msdn.microsoft.com/Forums/en-US/wfprerelease/thread/3aabc65b-dfda-48c8-b20e-cee0151059a6

WF4