Fine Tuning

When you first start practicing directing your thoughts on purpose, and therefore feeling good on purpose, a lot of wonderful things happen. 
First, you feel really good.  That feels amazing, and everything seems beautiful and easier and more fun.
Then, it's as if there were awesome things piled up behind a door and you opened the door.

People are nice, traffic disappears, something you wanted suddenly shows up.  Again and again, you get to see the manifestation of something you wanted.  At first, you don't even realize your change in perspective has anything to do with it.  Then as it continues to happen, you realize you are allowing all these things by your new attitude.

After a while, maybe a few months, it's common for manifestations to slow down. 
First, because you may have developed a habit of verifying your 'worth' by what you see you have manifested. Then you start to look for  manifestations.  Looking for something you can't see contains the negative thought of  'it's not here.'  Noticing it's not here brings more 'not here'  It also contains a negative thought of, 'I'm not doing it right', or 'I haven't earned, or learned it yet.'  Self-criticism is the most insidious block to positive manifestations.

Second, the negative thoughts you now have are much more subtle.

As you clean up and discard and replace negative thoughts and beliefs about various subjects, you inevitably leave behind smaller and smaller remnants of those negative thoughts.  Cleaning up, or replacing, those remnants is called 'fine tuning.'

It's harder to notice subtle negative thoughts. But once you notice them you realize you think those types of thoughts 10 or 15 or 20 times per day.

The easiest and most reliable way to realize what subtle negative thoughts you have been thinking is in your dreams.

When you wake up, stop and think, "What did I dream?"
Then "How did the dream feel?"

Dreams are the absolutely most accurate indicators of how you have been feeling the previous day (or days).

The content or characters or weirdness of the dream makes no difference; it's how the dream felt that is the key.
If the dream felt fun and adventurous, you're on the right track; keep it up!
If the dream felt scary or embarrassing or overwhelming or frustrating or angry, etc, you know very precisely what you have been feeling recently. Ask yourself what in your life has produced those feelings, but in a subtler way?  By that line of questioning, you can deduce what you have been thinking.
Then you can do a Focus Wheel about the subject, or use the Take the Bounce tool.

If you're unaccustomed to remembering dreams, tell yourself before you go to sleep that you intend to remember your dreams.

Another way to identify subtle negative thoughts is by noticing negative manifestations.
When anything negative happens, it is an accurate depiction of what you have been thinking.

Every single thing that manifests in your life is an indicator of, and an emotional match to,what you have been thinking.
If someone yells at you, if you stub your toe, if you get a medical malady.... or if your kid suddenly hugs you, or someone does something nice for you, or you meet someone at just the right time....  Each one of those things is a manifestation, and an indicator of what you have been thinking.
Once you identify that you have been having negative thoughts you can stop them by acknowledging the bogus nature of the thought.  And ALL negative thoughts are bogus.  Really. (See Ask And It Is Given, or any of the other titles in the reading list).

Three days ago I awoke to feelings of bliss and adventure and fun.  My snorkeling dreams had been so vivid and clear it took some time to realize I hadn't actually been snorkeling that night.  I celebrated the track of my precious day's thoughts!

The following morning I awoke to feelings of embarrassment.  Vivid dreams of being arrested were fresh in my mind.  I then did a little casting back to see what I may have been feeling embarrassed about.  A small army of random, tiny, insidious, shameful thoughts that I had had recently became clear to me.
I wrote them all down.  I then Took The Bounce on the first one.  It was easy to drum up thoughts that felt the opposite of embarrassment; of confidence and pride and competence and security.  Then I looked at the rest of the list and it all suddenly sounded ridiculous, which meant I no longer believed those old statements from my new point of view.   Perfect.  That's how you shift subtle thoughts.

Then last night I had dreams of fun social situations that felt like love and happiness and joy.  That means that I successfully 'cleaned up' the subtle negative thoughts I had from the days before.
That's how it works.  It never gets done and it gets more and more subtle.
You may never stop 'cleaning up' negative thoughts, but that's okay.  That's what you're here for.