For Site Columns, run the GenSiteColumnsXml command (using groupFilter helps get your custom ones), and then in the resulting xml, remove any columns that have the "Version" attribute. Then create your feature.xml:
and then put your site columns into your elements.xml:
For Content Types, do the same thing, only after pasting in from the GenContentTypesXml command, remove XmlDocuments Node from each ContentType:
That should do the trick!