I would use nmLVS with some HCells to define correspondence points, and crossprobe results using RVE and DESIGNrev. (All part of the Calibre suite, as that is what I work with here at Mentor.)
I did find a new appnote about using Calibre tools in Virtuoso to do LVS and all - maybe something there will help? It is MG576923, "Extraction and Simulation Within the Cadence Environment."
Hope that helps-
Sam.