It is true that there are about 6,000 Greek manuscripts of the New Testament, but one mustn't think this means there are 6,000 ancient Greek manuscripts out there containing something like a whole New Testament. Many of these documents are fragmentary, and many are late. Perhaps a good illustration of this would be to look over the documentary evidence for 1 Timothy 3:16.
A helpful tool for this sort of investigation is the Liste (German for "list") kept by the University of Muenster's New Testament Virtual Manuscript Room. A handy search tool for it can be found here:
Using this tool, it is possible to run a search for all Greek manuscripts which contain 1 Timothy 3:16. This yields 347 results. This means that of the approximately 6,000 Greek New Testament, over 90% do not contain 1 Timothy 3:16. This is not too surprising -- many of these "manuscripts" are fragmentary, and even of the larger ones most only contain a small selection of New Testament books.
We can narrow this 347 down further. As a slider at the bottom of the Liste search function shows that the search function by default includes manuscripts from anything between the beginning of the first century and the 1799. Let's sharpen our criteria a bit, and only search for documents from the first eight centuries of Christianity.
Now, there are only seven manuscripts that include 1 Timothy 3:16. Let us look at them in order. As we'll see, three of those manuscripts do not contain the most interesting part of 1 Timothy 3:16. So, for the textual criticism of this verse, we are down to four manuscripts from the first eight centuries.
Third Century: One Scrap...
First, in the third century, the there is a scrap of papyrus known as P133. To give a rough idea of what it contains, here's 1 Timothy 3:16 in English, as found in the ASV, with the parts that appear in P133 in bold:
And without controversy great is the mystery of godliness;
He who was manifested in the flesh,
Justified in the spirit,
Seen of angels,
Preached among the nations,
Believed on in the world,
Received up in glory.
In other words, if we were to attempt to "translate" such a fragmentary text into equivalent fragments of English words, this manuscript contains "yst ... ted in ... fle ... in ... s...t ... Se.. ...s ... Pre..ach...ed ... Be...iev.. ... Rec...iv... ...". In fact, we wouldn't even be able to know what this fragment was about if it wasn't for our already being familiar with 1 Timothy.
Fourth Century: One Manuscript...
Here and there, there are people who have placed the origin of Sinaiticus as late as the early fifth century, but here I'll go along with the dating found at the Liste website. As the list counts it, that papyrus P133 was the only copy of 1 Timothy 3:16 from the third century, and Sinaiticus is the only fourth-century copy. Below is a pair of images, taken from the Liste site, which show this verse. (The first image is taken from the bottom of a column of writing; the second image from the top of the following column.)
What is written in the large faded brown letters is rather unremarkable -- it is much like the text of the ASV which we quoted before. However, something interesting is going on in the fourth line.
In the fourth and fifth line, if we just translate what is written in brown, we find the expression "HOS EPHANEROTHE EN SARKI", or, "he who was manifested in the flesh". However, a later hand, in smaller black letter has written a theta and a sigma with a line through them above the word hos, "he who". This is a standard abbreviation for theos, or God. What the second writer intends here is that, instead of "he who was manifested in the flesh", we should read "God who was manifested in the flesh".
Fifth Century: Two (or Three or Four) Manuscripts...
Following the dating in the Liste, the fifth century gives us three solidly dated manuscripts: the manuscripts called Alexandrinus, Ephraemi Rescriptus, and Uncial 61. A fourth manuscript, Uncial 241, is dated to somewhere in the fifth or sixth centuries.
Alexandrinus...
Here is a snippet, from the British Museum's 1879 facsimile via Michael Marlowe's bible-researcher.com of Alexandrinus at this passage, with the critically important bit circled in red:
There is an unfortunate blurriness at the critical place, that makes me wish I had the manuscript in front of me. Since I'm not in that position, I'll have to rely on others who have had that experience. Unfortunately, there has been some disagreement among those who have seen it up close. Here is a quote from Samuel P. Tregelles, An Account of the Printed Text of the Greek New Testament; with Remarks on its Revision upon Critical Principles (London, 1854), pages 226-236, as reprinted by Michael Marlowe on his website:
Both A and C have suffered correction in this word; A in modern times, and C at a remote period. Such a change was effected by altering OC into ΘC [with a line drawn above] by introducing two little strokes, and then there was the contraction commonly found for θεος. The ink in which this has been done in A is sufficiently modern and black to declare its recent application, but it has been said that the trace of an original transverse line may be seen besides the modern black dot in the middle, decisive that the first letter is not O but Θ. Wetstein attributed this stroke, which in some lights is visible at one side of the O, to a part of the transverse line of the letter Ε on the back of the leaf. He says that it was only visible when he held it in such a position that he could see some light through the leaf. This was denied by Woide, who said (trusting to the eyes of others rather than his own) that the Ε was so placed that no part of it could be seen directly opposite to the O. Now I can state positively that Wetstein was right and Woide was wrong: for I have repeatedly looked at the place, sometimes alone, sometimes with others; sometimes with the unassisted eye, sometimes with the aid of a powerful lens: and as to the position of these two letters, by holding the leaf up to the light, it is seen that the Ε does slightly intersect the O, so that part of the transverse line may be seen on one side of that letter.
The opinion of Tregelles and Wettstein is also adopted by the transliteration over at the University of Muenster, and by NA28, where ος is given as Alexandrinus' original reading and θεος as the work of a corrector.
Ephraeimi Rescriptus...
Look at this for a moment:
This image is from the Bibliothèque nationale de France, via the University of Muenster: https://ntvmr.uni-muenster.de/manuscript-workspace?docID=20004.
If you're noticing that this looks like an unusual manuscript, you're not wrong. This is Ephraemi Rescriptus, in which the rescriptus means "re-written". Originally a text of much or all of the Bible, this codex had its biblical text scraped off so that sermons by Ephraem the Syrian could be written in. Today, a great many people are interested in early biblical manuscripts, and a relatively smaller number of people wish to read the sermons of Ephraem, and so this appears to be a historical tragedy. For a time, people could only squint at it and pull a few readings out, until, by means of chemistry, somebody figured out how to smear some kind of chemicals on it that would cause the original text to resurface. In this image, the original text appears blue, while the sermons of Ephraem appear in black.
I can read enough of the original text to know where the critical part of the text is. It's in the second blue line of the snippet above, which coincides with the first black line. The first "word" in that blue line is in fact a fragment, STERION, which I can make out, the last part of MYSTERION, "mystery". The next this I can make out is PHANEROTHE, which is most of the word EPHANEROTHE, "manifested". Unfortunately, between the two, I cannot make out either an OS or a THEOS.
I am assured by the University of Muenster, however, that, just as in the previous manuscripts we've looked at, the original reading here is OS, and that the hand of a later corrector is visible changing it to THEOS.
Uncials 61 and 241...
Unfortunately, Uncial 61 is fragmentary and lacks the critical word in 1 Timothy 3:16 that we are looking at here. The same is true of Uncial 241.
Sixth Century...
Claromontanus...
This is a very interesting manuscript. Instead of OS, it would appear that this manuscript originally had a single O, an omicron. This omicron appears to have been altered to look like a sigma -- compare it to the other sigmas in the same manuscript if you doubt this. Along with the alteration of O to sigma, someone has then written in a theta, and added a line over the top, creating the standard abbreviation for THEOS, "God".
This manuscript is unusual in that it has every other page in Greek and Latin, so that where the Greek reads some combination of O and THEOS, the Latin reads quod, which -- like Latin readings in general, supports the "he who" reading rather than the "God" reading.
Seventh and Eighth Centuries...
Nothing. There's nothing from these two centuries.
Ninth Century...
So far, in the first eight centuries, we've been able to find just four manuscripts. Two of them, just from images publicly available online, show that they originally read OS or O, and that later interference attempted to add the word THEOS ("God") instead. For two other cases, I cannot tell what is going on from the images, but scholars assure us that similar hijinks have been at play.
Now, in the ninth century, the list tells us that nine manuscripts are available, plus two that may either be dated to the ninth or tenth centuries.
Uncial 010: Codex Augiensis...
First is Uncial 10, the Codex Augiensis. Unfortunately, the University of Muenster is unable to share images of this manuscript with "non-experts" on the open internet. The University does, however, display a transcription, which tells us simply that the manuscript (in Greek) reads OS. However, the transcription is courtesy of the Museum of the Bible, an institution which I do not trust, so I would like to confirm this elsewhere if possible.
Archive.org has a facsimile of a transcription published by Scrivener in 1859, and here's the relevant part
If you notice the Latin, that's because Codex Augiensis is a bilingual manuscript. The Latin here is simple: quod. But the Greek is a bit more complicated. Like the Museum of the Bible, Scrivener here reads OS, but he puts a line over it, as if it were a divine name.
So what's in the original manuscript? I do not know. I am a mere non-expert, unworthy of seeing the facsimile.
Uncial 012: Codex Boernerianus...
Next is Codex Boernerianus, a weird document. It's in Greek, with a Latin interlinear inserted above the Greek words. Here's the verse, from SLUB Dresden, via the University of Muenster:
This is another one of those "mixed" readings. Looking at the letters themselves, the critical word is clearly OS, and the Latin quod above it confirms this. However, there's a small line over the O which makes it look as is someone is trying to mark this up like the word THEOS. Weird.
Other Uncials...
According to the University of Muenster, Uncials 018, 020, 044, 150, 151 read simply THEOS, as do miniscules 1424 and 1900. I am not allowed to see the facsimiles. Similarly, for Uncial 025, the reading is simply said to be THEOS, but a facsimile does not yet seem to be available.
Uncial 033 is missing the first letter of the critical word, so it simply reads S, without making it clear whether it reads OS or THEOS.
Conclusions...
This, of course, isn't a full examination of the evidence on 1 Timothy 3:16. But I was struck by a few things. First, how extremely few manuscripts there are before the ninth century, and how often it seems that the manuscripts have been tampered with -- though quite possibly by well-meaning editors. I was also struck by how, in the ninth century, a relatively large number of manuscripts suddenly appear, and they almost all suddenly have the reading THEOS -- although every darned one of those manuscripts is for some reason off-limits to amateurs.