If you install ScopeHunter via PackageControl it will help you discover the scope for the various parts of your code. Then you can add some of these scopes, and your chosen colours, to your theme-file.
But first I would test a few different themes - this will help to confirm that it is your theme that is letting you down. That is, that your theme isn't defining colours for the variety of scopes that you would like.
When you are checking the scopes for the various parts of your PHP code, if you believe that some are incorrectly scoped, then it becomes a bit trickier. This would mean that the syntax (PHP.tmLanguage) file is not working correctly - or is not exacting enough. Modifying this file to correct it can be a challenge
But perhaps someone, somewhere, has already modified/corrected the PHP syntax file and might offer it to you
Personally, I added a couple of PHP-specific colours to my theme, but I'm trying to ignore the formatting of PHP/HTML/JS combinations - because I suspect it would prove quite messy to fix.
"I'm here to save your life. But if I'm going to do that, I'll need total uninanonynymity." Me Myself & Irene.