To get this plugin to work with 3.1 take the following steps:
Admin areas:
modify bp-links-core.php line 313 (FIXED) (or approx) to read:
`add_action( ‘network_admin_menu’, ‘bp_links_check_installed’ );`
modify bp-links-admin.php line 27 (or approx) to read:
`add_action( ‘network_admin_menu’, ‘bp_links_add_admin_menu’, 12 );`
These two fixes add ‘network_’ to the admin_menu action to place it in the network settings (not the site settings) in a multisite arrangement.
There is a better fix for compatibility sake that is referenced here: http://bpdevel.wordpress.com/2011/02/24/updating-your-buddypress-plugins-for-1-2-8/ that allows for multisite and non-multisite compatibility (however I am running multisite so I don’t need the compatibility built in).
Colorbox/shadowbox fix:
Update the `jquery.colorbox-min.js` from http://colorpowered.com/colorbox/ (jquery was updated and likely broke this old library file.) The file is located in `buddypress-links/themes/bp-links-default/_inc`
This was just discussed at http://wordpress.org/support/topic/plugin-buddypress-links-shadowbox-not-working
Hope this helps. It got me back up and running. 
Thanks, @crazycoolcam it looks like it’s working. Thank you for your help. 