Upgrading Error with Plugins

Hi,

I just upgraded several of my wordpress sites at work. No Problems.

Then I upgraded a remotely hosted WP site and ran in to some issues with plugins.

1. Yes I did turn off all the plugins before upgrading.
2. The first error message I recieved noted the plugin.php file error lin #16. It also mentioned something about the file path Hmm? What could this be?
3. I tried editing this file and removing some plugins. Now I get this message.

“Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, webmaster@badriverwatershed.org and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.
Apache/1.3.34 Server at http://www.badriverwatershed.org Port 80″

The server I am running this on is a cpanel hosting site with fantastico. Here are some details
PHP version 4.4.1
MySQL version 4.0.25-standard
cPanel Build 10.6.0-RELEASE 158
Theme cPanel X v2.5.0

Much Thanks for any help!