What is the difference between "munafiqun" and "munafiqin"? Would it have been correct to only write either nouns without..

Assalamu Aleikum wa rahmatu lilahi wa barakatuh

A) I have notice that in the first verse of surah 63 (al munafiqun) they are two ways the nouns munafiqin  is written: the first is : MUNAFIQUN ("idha djaa'akal munafiquna...") and the second is MUNAFIQIN ("...wallahu yashadu innal munafiqina...") My question is:
a) What is the difference between "munafiqun" and "munafiqin"
b) Would it have been correct to only write either nouns without choosing the other? For example write: "Munafiqun" all throughout the surah or vice versa?

B) Secondly, the prophet Muhammed (pbuh) used to stop at the end of an ayah when reading the Quran. Did he also used to join two ayah together (or joining two words) when reading?Is it sunnah or farda to join ayah while
reading?
May Allah help you inshallah
Ma'a salam

Answer

Wa alaikum assalaam wa rahmatullahi wa barakatuh

A.  The words  and are examples of regular male plural nouns.  These nouns change from a  to a   before the last letter ( ) depending on the grammatical place of the word in a sentence.  If the regular male plural is  , such as the subject (doing  the verb), then it will have the , such as in the first aayah of surah Al-Munafiqoon: .
If the regular male plural is , such as being the nominative of the participle , as in the last part of the first aayah of the same surah: ,  then it will have the    . 
These words then change according to grammar and it would not be acceptable to change them around in writing in the sentence structure.

B.  The Prophet,  usually stopped at the end of an aayah, but the were times when he would join two aayahs together in one breath.  It is sunnah to stop on the end of an aayah.  It is allowed to join two aayahs together, if the meaning is appropriate, but it is not considered sunnah nor fardh to do so.  Allah knows best.
Wa assalaam alaikum wa rahmatullah.