Andrew,
 
Have you read about the mh.private.ini file - it controls a lot of how Misterhouse behaves for you. Also using the web browser follow Misterhouse->Misterhouse home->SetupMisterhouse->Common_Code_Activation and then untick what you don't want to run (such as deep_thought.pl). Of course you might not be able to do that without setting up you administrator password. So likely you will have to make some other changes - I would recommend a more common install - see below:
 
Your approach to copy and rename may be a good way to get wet and then throw away - but it's not a good way to set up Misterhouse so that it is supportable and will be easy to upgrade. see http://w3.misterhouse.com:81/faq.html#1_3__how_can_i_easily_upgrade_to_the_latest_version_of_mh
 
Most people have this big directory of misterhouse with all the code in it, and then use the configurations to turn on and off the bit they want to use, and their own customizations - which is why it's so powerful after you get over the startup hump - which seems to be a right of passage. But there are lots of friendly folk on this list to help you out ...
 
Jim