Since no one else answered, I’ll go ahead and do so.
1. SQL does everything in 8k pages which are grouped together into 64k extents. All reads and writes to the disks are done one extent at a time.
2. I’m not sure where that formula came from. Everything I’ve read from the storage vendors says set it to 64k.
3. I set it on all drives on all servers. Exchange, Oracle, SQL Server, File Servers.
4. No, setting the alignment does not effect the way Windows stores the files on the hard drives. It simply moves the first place that Windows writes to from the 33th block on the disk to the 65th block on the disk.
5. Windows 2003 64bit has the same 32k offset as the 32bit OS. Windows 2008 actually defaults to a 128k offset. This should be just fine as it is basically the same as a 64k offset with a 64k file written at the beginning of the disk.