Migrating an Access Database into SharePoint 2007

There is a PowerShell provider that I've heard some good things about. It's available on CodePlex; however, it doesn't yet support MOSS 2007. That said, I've found using the SharePoint object model sufficient. If you don't want to dig into the object model, though, I recommend both Gary LaPointe's stsadm extensions, and his newer PowerShell cmdlets for SharePoint. Both are available via his blog.

You're right... out of the box, having SharePoint groups with thousands (or even hundreds) of individual users will be an administration nightmare.

Unfortunately SharePoint doesn't sync AD users with with AD (profiles, yes. users, no.), so once you have manually add a user to a SharePoint group or manually grant permissions to an individual user, they will remain in Sharepoint for all time (until you manually remove them), even if you remove that user from AD.

If you assign permissions to SharePoint groups holding AD groups, you gain the benefit that once a user is removed from AD, they no longer have permissions on SharePoint. It is so much easier to manage group membership in a single location (with good tools) than it is to manage group membership twice.

Long story short, I would suggest trying to figure out the problem you are hitting with audiencing before I would suggest putting a thousand users in SharePoint groups. If you absolutely must do so, don't do it with out of the box tools... invest in Quests's Site Administrator for SharePoint (http://www.quest.com/site-administrator-for-sharepoint/)