There is an issue with Drupal 6 menu router rebuild which causes Drupal to time out with 404 pages or internal 500.
The following fix worked for me:
Install Drupal Tweaks, increase php memory, and mysql recommendations etc
http://drupal.org/project/drupal_tweaks
Download the following patches:
http://drupal.org/node/251792#comment-1831346
http://drupal.org/node/317775#comment-1491208
From command line copy patches to your root drupal directory.
cd to your root drupal directory and then apply the patches. Each time you will be asked where the file is for the patch and the actual path to the files to be patched will be provided in the command line. Just copy and paste each file path as presented into the prompt.
cp *.patch /home/drupal_directory/
cd /home/drupal_directory/
patch < no-router-blob-317775-56-D6.patch
patch < lock-251792-163-D6.patch
|--- includes/bootstrap.inc (revision 7577)
|+++ includes/bootstrap.inc (working copy)
--------------------------
File to patch: includes/bootstrap.inc
So in the above text you can see it gives you the path ‘includes/bootstrap.inc’. Just copy and paste that to where it says ‘File to patch:’. For each file it will provide you the correct path to the file assuming you are in the drupal root directory.
The final thing to do is to cp the lock.inc file which is created to includes/