In this post here on possible cause why the discovery wizard could run forever. Last week I faced a situation where the discovery wizard for deploying Linux agents and for deploying windows agents didn’t work. The setup topology was 2 management servers SCOM 2012 and one dedicated SQL Server 2008 R2 SP1 for the SCOM databases.
Microsoft just released the new Operations Manager 2012 Sizing Helper Tool. There was a similar Tool (basically it is an Excel sheet) for SCOM 2007 R2. But now there is also some guidance on Best Practices Disk Configuration, SQL Temp DB, High Availability and Network Monitoring. This tool can be found here .