Asalamu 3alykum brother Lobotomize
I would like to share my humble opinion regarding some of your questions which I must say that I think it will also open up other topics as we go along which will lead to a long discussion. So I will try to make it as simple and short as I can and forgive me if I fade off trying to elaborate on other related topics at the same time.
Here is a verse you have shared.
48:13 And whoever has not believed in Allah and His Messenger - then indeed, We have prepared for the disbelievers a Blaze.From what I understand or gathered of your inquiry is that Jews and Christians who do not believe in the veracity of the messenger Muhammad(pbuh) cannot be the Jews and Christians who are referred to in verses 2:62 and 5:69. So therefor those 2 verses must be in the past tense and cannot be in the present tense because it would shed tension on the verse above 48:13 since there is amongst Jews and Christians who presently do not believe in the messenger Muhammad.
So therefor to reconcile the three verses with each other one must read verses 2:62 and 5:69 in the past tense or its referring to the Jews and Christians who believe in the prophet Muhammad other wise it would be in conflict with verse 48:13.
I think first and foremost before going into detail about the verses mentioned, one must understand what a disbeliever is. Once that is acknowledged then I think the bigger picture regarding these verses can be drawn. Please see article below
[1].
We must remember that when the Quran characterizes and exposes the disbelief in Jews and Christians, it is doing so to
only certain specific ones. It also exposes the disbelief in Arabs as well
9:97-98. Which clearly does not mean all of the Arabs are disbelievers
9:99.
I find sometimes people fail to realize that the Quran was a live guidance to help aid the believers in a specific time and scenarios which had a set of specific circumstances. The Quran taught how to react and treat disbelieving Jews and Christian. Like some were not to be taken as friends etc. We should apply the same methods as the Quran teaches but it does not mean it will always be the same names and people.
Now the Jews and Christians that are spoken of clearly does not apply to all of them as verses like (3:113-114, 5:82-83, 7:159, 5:66, 3:75) verify that some are rightly guided. The Quran mention their names because the people who lived amongst the prophet Muhammad would of understood them and know exactly who the ones were, but to us today it would be to use the guidance and their names as an example.
Another evidence of the people who the Quran deals with is only time relevant to the prophet and his people is in verse 2:41. Also out of all humanity who were receiving the Quran at that time(God knows best their number and who many tribes), the Children of Israel were asked at that moment of time not to be the first to disbelieve which indicates there was a time period of reflection and a count down to who is going to show their disbelief first (2:41). This can possibly keep happening in the span of time over and over again. God knows best.
Verse 48:13 has a long context to it. The whole chapter is mainly regarding the Believers(mu'mins) and the Arabs who are living amongst the prophet Muhammad(pbuh).
After a victory for the prophet and the believers, God has exposed the hearts of those who stayed behind of the Arabs who did not go and help in fighting. Those people had assumed the prophet and the believers would never return back and also had evil thoughts which they harboured and therefor doubted and not truly believed in God and His messenger.
God had therefore cautioned them that for him who does not believe in God and His messenger, God has prepared a blaze for the disbelievers.
We need to look at the wisdom behind the verses, which acknowledge that its after the truth has been manifested one does indeed need to believe. These are warnings from God. No one is excused from this method. Not the people of the previous books or the people of the Quran.
What the Quran is manifesting, is that once truth has been made clear, which could be to any people at any time, then there is a time when humans must make their decision (7:34, 10:49, 13:7) . God knows best the time when truth has hit the peoples hearts and when they have believed or disbelieved.
So I do believe that the People of the Book who were living in the midst of the prophet and the ones The Almighty God has been speaking about in the Quran who heard the message clearly they were obligated to believe in the veracity of the messenger and the Quran. This is quite different though from Jews or Christians who never had the chance to read the Quran or even to give thought about it. There is also possibly in the time of the prophet also Jews or Christians who were so far away that they may of never heard the message. God knows best
I believe verse 2:62 and 5:69 is confirming to the readers or listeners of the Quran whether they lived in the time of the prophet or after him, be they Jews or Christians or believers of the final message(allatheena amanu) that who ever believes in God and the final day and does good deeds they shall not grieve nor shall they fear.
It really seems to be a refresher or confirmation to all those who have those attributes of belief that they shall not grieve or fear and seems to give that sense of comfort to keep their labels of Jews or Christians or those who believe. What it also seems to hint at, is that names or labels are not the concern, but its what is believed in the heart and that is what God looks for.
Although sometimes names are necessary in my opinion to distinguish certain people from others, but its what people do and how they act and believe which is the more important.
Another important point from the verses seems to indicate that the Jews and Christians who believe in the Quran and the messenger do not have to abandon their covenants and rites that was prescribed them. They were actually required to go back to their respective books in truth as you had clearly indicated 5:42-48.
It also seems to indicate to the believers of the Quran(allatheena amanu), that those Jews and Christians who are muslims(believe and God and the last day and do good) are like you in the sight of God and we are not to judge as they are branded in the same verses 2:62 and 5:69 with the Jews and Christians.
After all that has been said, the Quran is indeed the final Scripture given humanity which does claim to have the right over all others when faced with differences which in a way perseveres(muhaymin 5:48) the truth in other Scriptures . No one seems to be excused from believing in it after the truth has reached them.
But that does not mean that all of humanity will receive it at once or even ever (6:19).
6:19 Say, "What thing is greatest in testimony?" Say, " Allah is witness between me and you. And this Qur'an was revealed to me that I may warn you thereby and whomever it reaches. Do you [truly] testify that with Allah there are other deities?" Say, "I will not testify [with you]." Say, "Indeed, He is but one God, and indeed, I am free of what you associate [with Him]."That being said, I think one can clearly see how the holy Quran has been used to trial humanity from the time it was revealed to possibly the time of the Hour if God wills.
It seems like it will continue if God wills to reach out to all those who say they are believers, Jews, Christians, Polytheists, Idolators, Atheists, etc.
Only God will know who have disbelieved from those who have believed.
Also regarding verse 5:44, it is helpful to read it with the surrounding verses. I do not think this verse is indicating that the Torah is perfectly protected but it seems to confirm to the prophet Muhammad that if he chooses not to give them(Jews) judgement, there is no blame on him, as they have their own scripture the Torah which the prophets judged the Jews and the Rabbis and the Priests also judged by it and they were obligated to protect and obverse(istuhfithoo). So despite the fabrication of the Jews which is verified in other verses, there is still guidance and light in the Torah, which one would come to believe it does not lead to misguidance or idolatry in the sight of God, when He the Lord is telling them to judge by it.
Salam
[1] UNDERSTANDING 'KUFR' (DISBELIEF) FROM A QURANIC PERSPECTIVE
http://quransmessage.com/articles/understanding%20kufr%20FM3.htm