I was finally able to upgrade a custom fields install from mt 4.0 to mt 4.1 then to mt 4.2

This workflow was helpful, but not successful for me:

http://www.movabletweak.com/app/migratingcustomfieldsmovable_type.php

Here's the route that I took, with help from tech support:

1. duplicated the mysql database of original MT 4.0 install
2. uploaded the 4.1 to server
3. unzipped the install on the server
4. moved the mt-static directory to a new clean directory in the site root
5. updated the config file to point to the new mysql database * IMPORTANT *
6. Do not copy over the OLD CUSTOM FIELDS PLUGIN
7. logged in to the new 4.1 install (this prompted a database upgrade)
8. once the upgrade was complete THEN copied the CUSTOM FIELDS UPGRADE ASSISTANT PLUGIN to the CGI-BIN/MT/Plugins directory
9. logged in to the new 4.1 install again. This again prompted a database upgrade for Custom Fields Plugin Upgrade Assistant
10. it ran the the upgrade successfully.

If you are having trouble downloading the Upgrade Assistant Plugin from the developers site here is a direct link to the zipped file: http://code.sixapart.com/trac/mtplugins/changeset/590/branches/CustomFieldsUpgradeAssistant-bugfix?old_path=%2F&format=zip