The edits are no longer nessary in version SPF 3.0.x and up, WPMU databases are addressed correctly.
If you have edited your SPF 3.0.x instalation as per the SF 2.1 instructions, please re-upload a fresh SPF copy, as the edit may be causeing any errors you may be encountering.
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the error you are reporting is not a wpmu issue, but one that will effect all installs:
When clicking on internal forum pages you get a 404 error: This is almost always a problem with permalinks being mismatched in the forum and in WP-WPMU.
Using the Forum Tab in your dashboard, goto Manage Options.
You can set the forum page and slug under the first tab: make sure that there is no trailing space or slashes after the forum slug
If you run the forum in a sub page, also make sure that the parent page slug IS listed with a froward slah and then the sub-page slug (I.E. [parent-page/sub-page] )
Now we move to the last tab in the Manage Options section, “TOOLS”
The forum page slug is sometimes auto identified here, but it does need to be reset.
Click “update permalink” …you may or may not notice the permalink changing… then click SAVE OPTIONS. Saving options is required after this step.
You should now be able to click the “GOTO FORUMS” button and navigate your forums without error…
IF you continue to get the 404 error on internal pages of the forum then we have to begin looking at plugin and theme conflicts.