After installing, Drupal 6.2-dev becomes permanently unresponsive.

I have over 400 modules to install on the website I am working on. Some of the modules require jquery_update to be installed. I had jquery_ui installed at first and got good response time from Drupal. After installing, jquery_update brings the website to an impossible crawl. It even crashes IE8 and firefox 5 after getting stuck for some time. I have no idea where the problem is, but skinr requires dialog which requires jquery_update. A major part of the website is broken now. If I disable the module in the database directly and go back to the website, everything returns to normal. Any ideas on how to deal with this?