Epistemic status: provisional. Practical suggestions somewhat tested.
Two big functions of emotions: 1. motivation to do something that needs to be done, 2. bearing witness to truth. There may be other functions, but these two stand out to me right now.
If an emotion is neither practical nor truthful, it may be pathological. For instance, perhaps you feel pain over some past event (a trauma or a death). A certain amount of pain motivates you (to get out of a relationship or to seek new relationships, for instance). A certain amount bears witness to the truth -- you really were wronged, or someone who you know was really valuable is no longer with you. But beyond that, the pain is pathological.
How can you tell when a negative (or positive) emotion has crossed from truthful into pathological? One possible criterion is: does it keep you from doing what is necessary, in parts of your life more, or less, related to the emotion? Another is: does it keep you from intellectually or emotionally bearing witness to the truth? It may be possible to have a vivid pathological emotion toward a reality, which prevents you from having the one that bears witness to the truth. For instance, to be sentimental over a person rather than respectful, or triggered rather than receptive. Or, a pathological emotion can keep you from having the intellectual bearing-of-witness to a truth, perhaps in a different part of life. Truth is much bigger than just one truth. Given the complexity of truth, it may be hard to determine that a given emotion is not at all pathological, but you can more easily tell when it has definitely become significantly pathological.
There are far too many truths to bear witness to each of them, but the overall truth may be known, of all of reality, or sometimes of a society, life in general, or a person; and if a society never bears witness to a particular truth, that truth will be ignored, possibly preventing something of practical value to humans. Some truths are distant and we can have little responsibility for them, while others are things we see all the time, or have seen recently.
An emotion can fulfill one or both of the functions of motivation and truth in the area where it directly applies, but also interfere with a necessary action or bearing-of-witness to truth in another area, and thus be pathological.
Given what is written above, thoughts are in much the same situation as emotions. Thoughts can: 1. motivate necessary action; 2. bear witness to a truth. And there may be other functions that don't immediately come to my mind. Otherwise, thoughts are pathological. And one way to identify a pathological as opposed to truthful thought is one that interferes with motivating necessary actions, or which interferes with bearing witness to another truth. Like with emotions, it's hard to be sure a thought is not distracting from all other truths which might be more necessary to contemplate than it, but sometimes it's not so hard to identify a thought that keeps you from thinking another specific truth that is more necessary. A thought can fulfill legitimate functions but be pathological for interfering with the action or bearing-of-witness in other areas.
It may be more often useful to think in terms of "what practical steps or overall truths, or relevant particular truths, am I missing?" rather than "which of my thoughts and emotions are pathological?" If you are more successful with the first issue, the second is less relevant.
You can't get the overall truth of a formulaless being (such as a human being or God) by no matter how extensive a dissection. It can be helpful to meditate on people's qualities, but not necessary to figure out what makes them tick, in order to get their overall truth. In fact, being overly concerned with the mechanism risks getting lost in the poetry of something rather than its reality.
This all could be seen as a kind of therapy, and pursuing it can have a therapeutic effect. But the drive to therapy itself can be a pathological thought pattern (an obsession over health and well-being). So it is good to focus on truth and usefulness, more so than therapy, even if the outcome is therapeutic. (The therapeutic could be seen as a form of what is useful.)
Thinking and feeling (as well as sense perception) can be part of "seeing". Seeing a thing to see its truth is different than seeing it for the sake of personal self-interest, usefulness, place within some kind of lawyerly case, or enjoyment. The seeing itself is different.
Mindfulness has something to do with seeing the truth of something, but isn't necessarily the same. Mindfulness may or may not be pursued simply to see the truth of things, and I'm not sure from my limited knowledge of it whether mindfulness has as broad a scope as seeing the truth of something.
Literary poems (by one definition) use words to try to create an intuitive whole, and can bring up just about anything in the process. Seeing the truth of something can work the same way. A literary poem may try to accomplish something, have an agenda, but seeing the truth does not, beyond seeing the truth. A literary poem uses words, but seeing the truth of something doesn't have to. What is important is, in one whole, to think, feel, experience, but also intuit, in order to experience the truth of something. This can be seen as really listening to a simantic word, on the "face" or "side" of it that you have experienced.