How to read and study the Qur'an?

In undertaking this work (, I had to completely re-assess commonly accepted ideas and prevailing thought. Whilst this task was demanding, my approach was relatively simple, which anyone can follow. When I study The Quran, I often consider the following:
Am I for/against a certain outcome?

If I sense I am, I try to understand why to free myself from this bias/shackle, so I can truly let the message tell me what it is saying, rather than me tell it.
The perfect way is only difficult for those who pick and choose. Do not like, do not dislike; all will then be clear. Make a hairbreadth difference and heaven and earth are set apart; if you want the truth to stand clear before you, never be for or against. The struggle between "for" and "against" is the mind's worst disease. 
~ Zen commonly attributed to Bruce Lee
Critical Thinking Lessons
Is my understanding of the verse logical?
If God is the author of The Quran, then it will contain the utmost precision and logic. A firm grasp of this aspect will significantly improve the chances of gaining an accurate understanding.
Logic, Rhetoric, Legal Reasoning in the Quran: God's arguments (book)
Logical Fallacies information
Does my understanding conflict with another part of its message?
If so, it must be rejected. This includes specifics and its general principles and limits. Cross-reference becomes a must.
Root and Word cross-reference resource
Topical Index of Quran

Does my understanding fit the grammar?
Quite often, seemingly small differences in grammar can make a significant difference to the interpretation.
Arabic Through Quran (book)
Arabic: an Essential Grammar (pdf)
Is my understanding practical?
It should be considered if the resulting understanding is actually possible to enforce or implement practically in the real world.
Are there different views on this issue?
Consultation of multiple sources/books and discussion with others is an important aspect in understanding. Quite often, others will highlight issues you may not have thought of. Be open, weigh and consider them.
If my knowledge is so that I cannot conclude anything then I should not, as there is no harm in taking one's time. Gaining knowledge is a continual learning process, therefore patience and gradual acceptance is key. When unsure, turn to God and continue to do good and be good. Do not rush an understanding, as it is possible you are not ready for it [5:101, 20:114]. When you are in a God-conscious state of mind, you will be more in tune to His message, thus understanding of it will become much easier.
What does The Quran say?
The following is a brief list taken directly from The Quran on how to process information, read, study and understand it:

16:98 - seek God's spiritual aid, away from the forces of satan/opposition (e.g. emotional instability, personal desire, self-delusion, arrogance, prejudice, deviation).
3:7 - ground oneself in solid principles, maintain sincerity.
6:56, 13:37, 30:29, 42:14-15 - be wary of following desires as opposed to following God's revelation.
3:195, 4:135, 5:8, 8:61, 28:54, 42:40 - remain true to its principles of justice, equivalence, fairness, compassion, opting for the good/better response etc.
6:114, 12:111, 17:89, 16:89, 18:54, 39:27 - try to utilise and appreciate its complete system of concepts.
4:82 - anything from God will not have contradiction/inconsistency/variance. This also applies to our understanding as well. If we formulate a correct interpretation of The Quran, we will find that everything falls into place. This is one of the most crucial criteria.
5:101, 20:114, 25:32, 73:20, 75:17 - do not rush our learning, read what is easy of it, gradually build knowledge and acceptance to strengthen one's heart, and ask God to increase our knowledge.
73:4-5 - in order to receive a weighty or profound word or saying, we need to arrange the likenesses in The Quran, e.g. cross-reference concepts/words/topics.
21:10, 30:30, 41:53, 51:20-21  - its information and teachings should map to our reality (within our psyche, experience and to the furthest horizons). All signs, internal and external can point to the truth of it and act as a verification mechanism.
29:20, 3:137, 3:190-191, 45:3-4 - knowledge of archaeology/biology/physics/history/sciences/philosophy etc will all help to better understand it.
6:75-79, 21:57-67, 36:78-79, 21:22, 23:91, 2:258, 12:26-27, 22:5-6, 2:260 - promotes logical thinking.
8:22 - strong affinity towards use of reason.
49:6, 45:24, 6:116, 53:28, 2:111, 21:24 - disapproves of conjecture/guesswork and promotes examination of evidence.
34:46, 6:50, 2:219, 3:191, 10:24, 16:44, 30:21 - shows the importance of reflection, to deeply consider/think.
47:24, 23:68 - "tadabbur" means to ponder over something giving careful consideration to its consequences.
41:44 - language is not a barrier, belief/acceptance of it will help understanding.
25:33, 17:41 - it contains the best response/explanation.
39:18, 42:38 - listen and consider other views and follow what is best of them.
6:116, 12:106 - majority opinion means nothing.
2:2, 3:138, 10:37 - a guide for the god-conscious/forethoughtful, there is no doubt in it, thus understandings which raise doubt about it must be carefully reviewed.
17:45-46 - to not believe in the hereafter can act as a barrier to its understanding.
12:3, 18:54, 17:89, 7:176, 12:111 - look to its internal examples, stories within it give us lessons, it is a clarification for all things.
2:170, 7:28, 6:112, 7:70, 26:74, 43:23 - advised not to blindly follow the teachings of our ancestors.
17:36, 39:9 - seek knowledge, verify, use your God-given senses.
25:1, 2:185, 6:114-115 - it is the criterion with which to determine/judge.
7:204 - give it full attention, focus.
19:76 - it increases guidance for the guided, i.e. those who continuously turn towards, seek it and follow it.
22:46, 7:179 - open your heart and mind.
13:17 - any interpretation must always be understood in a way that is focused on benefiting mankind and our development.
15:1, 17:82, 36:2, 2:97, 45:20, 10:57, 56:77, 85:21 - any understanding should reflect its attributes, such as: wisdom, mercy, healing, noble, glad tidings, blessing, clear etc.
17:9 - guides to what is straight/upright/establishing.
20:2 - it has not been sent to make us suffer unnecessarily, thus any interpretation should bear this in mind.
22:54, 34:37 - those closest are those who believe and do good works, implying god-consciousness/righteousness and understanding could go hand in hand.
56:79 - purity of mind/heart will grasp it. Work on this aspect of oneself as you seek guidance.
3:79, 75:18 - apply what you learn/know.
39:27-29 - variance rejected, no crookedness, one consistent source is the preference.
4:87, 31:6 39:23, 77:50 - stick with a solid/proven source, not a baseless narration/hadith. The Quran is the best, most truthful and only obligatory hadith.

May your studies be fruitful.
Wakas (