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What is the difference? Why did Allah command the angels to prostrate to Adam? How do you know in your heart that it was not in the same spirit as you yourself prostrate to Allah today?
Because it's a given and a simple fact in Islam that worship is only for Allah . Thus , if we see a sign or a narration that seems as if it defies that , we take the clear one . And as the sign said , only the ones whose hearts are astray follow the unspecific .

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Are these signs you speak of the reason why many muslims seek clarification on the Quran from scholars? I mean to make clear to them what maybe was not clear from just reading it for themselves.
Let's be honest , commoners don't know that much . There are basic things in Islam and it is impossible for anyone not to know them . Examples are the five pillars of Islam and six pillars of belief . Beyond that , there can be matters unclear to the commoners and that's where they should ask scholars . It isn't that the message is impossible to understand , but people differ in their abilities . You also ask your popes about what you don't understand , right ?

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In your text above what inference am I to take from the words in [ ] am I to take it these words are added for clarification and not part of the original text?
Indeed . But that's because a sign that is clear when said in Arabic isn't necessarily as clear when translated to another language and that's why they are used to clear things . In the original language , you don't see such brackets . Maybe in some explanations only though .

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Satan's mission is to turn away as many people from believing the death and resurrection of Jesus is true.
Your belief .

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As for the prostrating of angels, and since angels are higher than humans,
!!??

That might be in your religion , but not in ours . Angels were created obident and they never disobey Allah :

66:6 O you who have believed, protect yourselves and your families from a Fire whose fuel is people and stones, over which are [appointed] angels, harsh and severe; they do not disobey Allah in what He commands them but do what they are commanded.

Humans however have the free will and can recognize the path or rightiousness and falsehood . If a human chooses the right path , he/she is above angels , and if they don't , they are below animals .

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I would like to ask you Muslims how is the prostrating you do five times a day different than the angels prostration before Adam? There is no way you can get non-Muslims to believe that prostration is not a form of worship.

And I suppose that the Koreans , Japanese , and maybe Chinese people who bow to each other out of respect are worshiping each other ?!