I have created a custom aspect for section called wsageSize. This shows up fine in share and in the alfresco node browser. Why is not available as part of section.properties? Are these values hard coded from SectionFactoryCmisImpl?
This is due to WQS using CMIS when retrieving sections, and CMIS not being able to return arbitrary, "unknown" properties via a query. In 4.0 this is resolved so that all properties of sections are returned (much the same as for assets).
Yes, you would basically need to replace the query and the buildSection method. I've just looked at that class and I've noticed that we haven't done a very good job at making it extendable which is unfortunate. Again, apologies for not making life a touch easier for you.
4.0 is out in community form already. I believe the planned date for the Enterprise release is early January.