Thank you for your post.
Are you able to get to the Test page?
Were these original PHP files created with FileMaker's PHP Site Assistant?
Move the original files to another folder (desktop) temporarily, and see if you can create and use the PHP Site Assistant with your database file.
Other than that, it sounds like you have done everything else correctly.
Going from 10.5 to 10.6 (both Desktop and Server) upgrade the default PHP installation from 5.2.x to 5.3.x . This is a fairly major PHP upgrade that did broke a few things. Since you said that you backup your solution's files, I'm guessing somewhere in there is something that got broken.
Check your php.ini file see if it is still displaying errors.