Well … as I said the first step is to Append the quads to a new Mesh. This yields one Mesh that either has DisjoinedPieces (Islands so to speak) or not. In your case yiels one Mesh. Then a Vertices.CombineIdentical Method should (in theory) yield a Mesh where the Vertices Count equals the TopologyVertices Count. That said Vertices are “Points3f” on a per MeshFace basis while TopoVertices are “Points3f” on a per (Disjoined) Mesh basis.
Anyway … if you want some “other separation and/or result” (meaning other naked edges than the ones from the standard GetNakedEdges Rhino Method ) you should provide explicit rules for that action (or mastermind Mesh Split ways via case specific edge rules/planes/splitters/cats/dogs/etc etc). These rules MAY are valid for the Append phase as well (i.e. avoid dating the same girl twice). That said the more rules use Mesh Connectivity (VV/VE/EV) the better (and way faster).
But in general this 48K collection of quads is chaos. Instead of Reverse Engineering (and reinventing the wheel) I would strongly advise to create the OEM Mesh in a far more rational way.