Not sure what you are saying here – “I do still have a bit of red showing, certain other changes must need to be done via manual edits, yes”. Are you seeing an error message? If so, what is the error message?
For php errors occurring in other plugins and themes take a look at this forum topic as a starting point: http://forum.ait-pro.com/forums/topic/how-to-troubleshoot-php-errors-php-errors-in-your-php-error-log/