Well, I think I've got it fixed. Amazing what you can do when you read the instructions! I first used mkext tool to make an Extensions.mkext of the extensions in the /Extra/Extensions folder, but that didn't solve the problem. But, after re-reading the guide, I ran the pfix utility as root, and it cleaned out the system caches as well as fixing permissions, and now everything is working OK! Thanks again for the great guide!