After nearly a hour of searching for an annoying bug (which turned out to be a new statement one line outside the loop it should have been in)....Multi-Regions in a single instance work, there is no Grid mode communication, so it can only be tested in sandbox mode right now.

All you need to do is put .xml files for each region you want to be ran by the single server inside the "bin\Regions" folder (make sure none of the settings in those .xml files conflict with each other) and then startup the server and login, Any neighbouring regions that are being ran in the instance should show up.  (However there is still no movement or anything) 
Now time to refine the communications interfaces!

1 files changed, 1 insertions, 0 deletions

diff --git a/Common/OpenSim.Framework/Interfaces/IClientAPI.cs b/Common/OpenSim.Framework/Interfaces/IClientAPI.cs
index 78be30a..810345f 100644
--- a/Common/OpenSim.Framework/Interfaces/IClientAPI.cs
+++ b/Common/OpenSim.Framework/Interfaces/IClientAPI.cs
@@ -84,6 +84,7 @@ namespace OpenSim.Framework.Interfaces
         void SendRegionHandshake(RegionInfo regionInfo);

         void MoveAgentIntoRegion(RegionInfo regInfo);

         void SendAvatarData(RegionInfo regionInfo, string firstName, string lastName, LLUUID avatarID, uint avatarLocalID, LLVector3 Pos);

+        void InformClientOfNeighbour(ulong neighbourHandle, System.Net.IPAddress neighbourIP, ushort neighbourPort);

         AgentCircuitData RequestClientInfo();

     }

 }