Sorry... I figured it out!
Here's what I did.
For .htaccess for site 1. If you have 2 import logs, but kept the IDs from import1, replace the first import log/site with VBSEO Hierarchy 001 and vBulletin 4.*:
[code]
RewriteRule [^/]+/([\d]+)-.+-([\d]+).html http://hostname/showthread.php?t=$1&page=$2 [NC,L]
RewriteRule [^/]+/([\d]+)-.+.html http://hostname/showthread.php?t=$1 [NC,L]
[/code]
with:
[code]
RewriteRule [^/]+/([\d]+)-.+-([\d]+).html http://hostname/threads/$1/page-$2 [NC,L]
RewriteRule [^/]+/([\d]+)-.+.html http://hostname/threads/$1 [NC,L]
[/code]
This directly redirects VBSEO threads without going through 301config.php.
301config.php should list the 2nd log and the 2nd site should have the first set of rules (going to showthread.php).
I hope this is useful if anyone makes the same mistake I have.
