Since the ‘Custom Salesforce JavaScript’ buttons aren’t going to be supported in Lightning, I went ahead and followed Paul’s instructions from this post last year: https://community.skuid.com/t/passing-id-from-skuid-page-to-conga-composer-error
Works great, the only thing I was not able to do was use the ‘reportId’ paramater in the snippet. So any Conga Buttons that used reports, I built Conga Queries and use the queryid parameter.