Sounds like the database being large is a red herring. Exchange 2010 supports up to 64TB databases and the max recommended is 2TB. I've seen a lot of really large databases that haven't had stability problems. So your issues may be related to something other than large database size.

You can use the default or a named instance. In the Topology Builder when defining SQL Backend, it'l have a radio button to use the default instance and another radio button to enter the name of the instance.

If you perform step 5 and DAC is enabled on the DAG before you simulate the failure, when the Primary Site comes back up, those servers will not mount databases since DAC is enabled and cannot contact the rest of the DAG Servers.

Because that's the wrong -Identity. Look at my original post and you'll see the format.

Check all the other services.
Get-WebServicesVirtualDirectory -Identity IdentityHere | FL InternalURL,ExternalURL
Get-OABVirtualDirectory -Identity IdentityHere | FL InternalURL,ExternalURL
Get-OWAVirtualDirectory -Identity IdentityHere | FL InternalURL,ExternalURL
Get-ECPVirtualDirectory -Identity IdentityHere | FL InternalURL,ExternalURL
Get-ActiveSyncVirtualDirectory -Identity IdentityHere | FL InternalURL,ExternalURL

Sounds like firewall rules to the VPN segment are blocked. Peer to Peer audio calls will use ports 1024-65535 TCP/UDP. VPN segments to FE for Conferencing should have 49152-57500 open for MCU Audio/Video/Conferencing.

You won't be using the FSW since you'll have an odd number of nodes. You can see in the Visios (and I do mention it in the text) that there is no FSW due to there being an odd number of nodes. You would still specify a FSW though as you only temporarily use the FSW as you build the DAG when having the even number of nodes or during failback as you add the primary site's DAG members back into the DAG when restoring service to the Primary datacenter. Once you add that third node back, the cluster automatically switches to Node Majority instead of Node Majority with Witness when you only had 2 nodes.

No, don't use a hidden share. I've had another person try this and I had to fix it as there were a ton of issues with it.

That's after you have Lync deployed. You merge topology and then import configuration.

Did you do the following?
1. Install Topology Builder Tools
2. Definite Enterprise Edition Front End Topology including the File Share and SQL Server it talks to
3. Publish Topology which creates the Central Management Server Databases and Front End Databases on your SQL Server?

The above must be done in an Enterprise Deployment to allow you to run Install Location Configuration Store on a Front End Server which installs SQL 2008 Express on the local Front End Server and creates a copy of the CMS (xds database) on the local server's SQL Express install.