Installing the ESB Toolkit 2.0 by following the official documentation is pretty much a task doomed to fail. There is however quite a number of guides available on the net. One of the better ones I've found is from Quicklearn: Getting up and running with BizTalk ESB Toolkit 2.0.
This one helped me with a basic issue that caused some grief.
After importing and installing the Core and Itinerary msi packages, I tried to run the Management Portal installation script Management_Install.cmd which worked half way before spewing out a ton of error messages.
I started looking at this issue and noticed that a number of exceptions came from IIS related components, for example: "Property 'AppPoolIdentityType' cannot be found on this object; make sure it exists and is settable.".
It seemed I had missed to enable IIS 6.0 extensions properly. The ESB Toolkit uses IIS 6.0 calls and these components are not installed by default when adding IIS 7 in Windows 2008 Server.
Later on I found myself with a minor issue when deploying the BAM activities.
Deploying View... ERROR: The BAM deployment failed.
OLE DB error: OLE DB or ODBC error: Cannot open database "BAMStarSchema" requested by the login. The login failed.; 42000.
Clearly a better error message than before, so I added the appropriate account to the databases.
CREATE USER SQLService FOR LOGIN [W1BTS3\SQLServiceAccount]
EXEC sp_addrolemember db_datareader, SQLService
With this change, the deploy was successful.
I'm still stumped on why the installation of the toolkit is so badly documented and lack a proper guide since the amount of settings, scripts and packages to handle is quite vast and it's so easy to miss a required setting/permission/whatever that will make at least parts of the installation process to fail.