Device.DrawIndexedPrimitives( Direct3D.PrimitiveType.TriangleList, Face.Array.VertexIndex, Face.Array.MinimumIndex, Face.Array.MeshVertices, Face.Array.MeshVertexIndex, Face.Array.MeshVertices / 3 );
Everything except MinimumIndex is supplied in the BSP file. All I had to do was load the "Vertexes" lump into a vertex buffer and the "MeshVerts" lump, which is just integer indices into "Vertexes", into an index buffer.
Also fixed the problem I was having with the leaves. All that was wrong was that I was loading the wrong lump. So I'm off to try and implement the PVS system.