Here's a bit more narrowed down guide I use:
1) /scripts/updatenow
2) Select MySQL version 4.1 in WHM Tweak Settings
3) /scripts/mysqlup
4) Add old-passwords under [mysqld] in /etc/my.cnf
5) Restart MySQL
6) /scripts/perlinstaller --force Bundle:
BD::mysql
7) Set MySQL root password in WHM
8) easyapache/buildapache
9) /scripts/upcp --force
You can also try out my open source program I'm working on to secure and optimize some parts of a cPanel server (if you're running a Red Hat/Fedora/CentOS product). Helps with the MySQL 4.1 upgrade and much more. All it doesn't do is set the MySQL root password and buildapache/easyapache. I've used it on my servers and many other people used it and reported it worked fine for the MySQL upgrade as well as lots of other things. If you want to give it a try, run the following command: