The InfoPath SDK had good setup documentation. As a Windows Server 2003 I have spent energy (and several weblog post sessions) on IIS configuration issues. I found the following excerpts particularly dear to my recent W2K3 experiences.
...For IIS 6.0 in Windows Server 2003, the Application pool list box should be set to DefaultAppPool. The default user for that application pool is the local Network Service.
...In Windows Server 2003, you must add the IIS Worker Process Group, with the permissions check boxes selected for Modify, Read & Execute, List Folder Contents, Read, and Write. This group includes the local NT Authority\Network Service user. Click Add, and then select the local system name (the computer name) for the Location in which to search for the user. Enter IIS_WPG, and then click Check Names. The group [system name]\IIS_WPG should then be added.