When you get a internal server error with cpanel/whm it usually means your perl is not up to date on your server.

So first I would update that then try some of these other tricks:

Make sure you’re running Perl 5.8.8 by typing this: check perl -v (make sure it says 5.8.8)

If you see 5.8.7 or something else, follow these steps:

1. wget http://layer1.cpanel.net/perl588installer.tar.gz
2. tar xfvz perl588installer.tar.gz
3. cd perl588installer
4. ./install
5. /usr/local/cpanel/bin/checkperlmodules

If you still have a issue try this:

1. Kill any upcp process that may still be running
2. /scripts/fixeverything
3. /usr/local/cpanel/bin/checkperlmodules
4. /scripts/upcp –force
5. /etc/init.d/cpanel restart

If you still have a issue then try this:

1. Upgrade YAML::Syck and File::Copy::Recursive:
2. /scripts/realperlinstaller YAML::Syck
3. /scripts/realperlinstaller File::Copy::Recursive