PHP Errors When Enabling MSM

I am trying to get an existing EE site working with MSM. I upgraded the site earlier from 2.1.2 to 2.9.3. Once that was working, I then installed MSM 2.1.7. When I enable MSM in the CP I get several PHP errors:

Message: apc_delete_file() [function.apc-delete-file]: Could not stat file /nfs/c10/h04/mnt/123456/domains/domain.com/html/system/expressionengine/config/config.php, unable to delete from cache. Filename: core/EE_Config.php Line Number: 1222

Message: Cannot modify header information - headers already sent by (output started at /nfs/c10/h04/mnt/123456/domains/domain.com/html/system/codeigniter/system/core/Exceptions.php:170) Filename: core/EE_Input.php Line Number: 213

Message: Cannot modify header information - headers already sent by (output started at /nfs/c10/h04/mnt/123456/domains/domain.com/html/system/codeigniter/system/core/Exceptions.php:170) Filename: libraries/Functions.php Line Number: 446

Once this happens, trying to access any page on the site gives “Site Error: Unable to Load Site Preferences; No Preferences Found” messages. Disabling MSM in the config.php gets the site working again, but how do I complete this so that MSM is working?