I used AutoSPInstaller to setup my production SharePoint 2013 farm on top of Windows Server 2012 using SQL Server 2012. I did not install Office Web Apps (yet). I also did not install the workflow service. I did a fully offline installation. I ran into two issues
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I had to stage my servers with .Net 3.5.1 before I could run AutoSPInstaller. Note that this was discussed in another thread and has since been remedied to be compatible with offline installations.
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I did not use the default search index file locations on my servers and ran into permissions issues while using a least privileges approach. I do not think this has anything to do with AutoSPInstaller but is a SharePoint issue. I corrected the issue by temporarily giving my Search Service Account local admin rights on the servers that host the indexes and reconfigured the indexes appropriately using PowerShell.