Crawl not indexing main site or document libraries on new Sharepoint 2007 server

I recently migrated my SharePoint 2007 from a single server running Windows 2003, SQL 2005, to a 64-bit farm running Windows 2008 and SQL 2008.  Everything appears to be working fine, but search refuses to crawl anything other than the main site and personal pages.  All other sites and subsites are just ignored, do not crawl and do not error.  The account the search runs as has read control over all the sites.  I extended the site to a different zone using a different port and ntlm authentication, and got exactly the same results.  None of the sites are host-header based.  

What can I do to force SharePoint to crawl my remaining data?  


Try 1> check the site and give read permission access to default crawl account.
Try 2> reset the site content from the SSP search administration page. Even before starting the crawl process add some documents to site document library.
Try 3> Extend the site to a different zone with NTML authentication and try to crawl that site.
Try 4> Create a web application without hostheader on none 80 port. and try to crawl that site.
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remove the main site crawl from the default content source definition
create a new content source named mainsite using the "sharepoint sites" type and the sps3://mainsite.url or sps3s://mainsite.url
ensure that the "Everything under the host name for each start address" option is selected


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msCCareAuthor Commented:
Here is what I did to correct the crawl:  

First, I changed the Default content access account to be the same as the web application pool for the SharePoint site.  My infrastructure was such that I had a separate web, app, and sql servers.  I enabled web services on the app server, made that URL the default, and the web server and shared name alternates.  Then I deleted the "mainsite" content source, and created a new one, with the full URL (on the new app server sharepoint site I added) of the specific site I was trying to index, with these settings:

name:  mainsite
type:  sharepoint
url:  http://NETBIOSNAME/sites/SiteName/
setting:  crawl only the sharepoint site of each start address

Ran a full crawl, and everything indexed fine.  
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