Thank you for this searching question.  First, let me say that I read and normally use the KJV here on Answers From the Book.  I have used this Bible all my life and am most familiar with it, as opposed to other versions of the Bible.  With that said, I also want to point out that I am not a “KJV ONLY” person.  I do love the language of the KJV, but I often compare others versions, and constantly use Strong’s Concordance to get a sense of the actual meaning of words used when it is not perfectly clear.  I do not totally promote one version over another, but would caution all readers to carefully consider different versions when seeking the true meaning of the Word.

Let’s look at a couple of the verses you cited from the NIV Bible as being deleted:

John 5:4 says, “For an angel went down at a certain season into the pool, and troubled the water: whosoever then first after the troubling of the water stepped in was made whole of whatsoever disease he had.”

NIV does not include that verse.

NASB includes the verse, but has a note that reads, “Early mss do not contain the remainder of v 3, nor v 4.”

NKJV includes this verse but includes this note: “NU-Text omits waiting for the moving of the water at the end of verse 3, and all of verse 4.”

Matthew 17:21 says, “Howbeit this kind goeth not out but by prayer and fasting.”

NIV does not include that verse, but has this note: “Some manuscripts include here words similar to Mark 9:29.”

NASB includes this verse but has this note: “Early mss do not contain this verse.”

NKJV includes this verse but has this note: “NU-Text omits this verse.”

It’s interesting to note that the INTERLINEAR GREEK-ENGLISH NEW TESTAMENT, by Nestle and Marshall (a Greek NT with the corresponding English words) omit both John 5:4 and Matthew 17:21.

So, what are we to think about this?  As I stated earlier I encourage you to compare different versions of the Bible, use a Strong’s Concordance, and if you can get one, get a Greek-English New Testament that will show if particular words or verses are in the oldest manuscripts.  I have read through many translations and have never seen where a truth was lost because of these controversial verses.  The Lord has been very faithful to preserve His Word, but it may require us to ‘dig a little deeper’ at times to find out if omitted verses were really in the older manuscripts.  With that being said, I do use these verses that are in the KJV.  Even as no truths are lost in the ‘main’ translations, neither are truths misrepresented in the ‘main’ translations.  I cannot comment on the validity of many of the versions of the Bible because I have not spent a lot of time comparing different versions.

I hope this is helpful to you.  For more on this subject, please click on these links: