Hi Wes,
Before you make any changes, go over this document and make sure your cards are compatible with table-5 in this link
http://www.cisco.com/c/en/us/products/collateral/interfaces-modules/catalyst-6500-series-supervisor-engine-2t/data_sheet_c78-648214.html
As far as removing the second sup in your chassis and putting a new sup and copy the config across, that will not work, because in order for the sups to form an SSO, the 2 sups in the chassis must be exactly the same. Migrating configs from stand-alone switches to VSS is not a straight forward process because when you convert to VSS all your port numbering will change.
HTH