Firstly, we need to point out that the New Testament manuscripts are copies and copies of copies; they are not independent texts that have been written by original authors. Most of these manuscripts were copied many centuries (some over a millenium) after the writing of the New Testament. Moreover, with regard to the Greek New Testament manuscripts that are available, some 80-90% represent the Byzantine or the 'Majority' text which is almost universally considered to be the worst text-type. Bearing this in mind, even if it is true that the manuscripts are 99% the same, this is not reassuring considering their poor quality. But the modern day textual critics seem to give quite a different picture of the accuracy of the New Testament. For instance, the committee of textual critics for the United Bible Societies' The Greek New Testament suggested textual certainty to be about 83.5% (which is way off from "99%" agreement between the New Testament text in the manuscripts).
The second issue is with regards to the differences simply being in grammar or spelling. This is unfortunately being too hopeful. In the earliest Christian periods, the professed followers of Jesus were engaged in intense polemics against each other. In this highly charged atmosphere, accusations of moral, ethical and theological corruption rifled back and forth, with various parties accusing the other of corrupting and fabricating 'scripture'. For example, an "orthodox" presbyter of Asia Minor owned up to forging the Apostolic Constitutions and III Corinthians. In his defence the deposed presbyter claimed that he did it "out of love for Paul." In fact, the textual history of the first three hundred years of the New Testament is described by the textual critics as "the period of relative freedom" or "the period of relative creativity." During this period the majority of changes to the text of the New Testament, both accidental and intentional, originated.
The New Testament scholar Harry Gamble says:
Complaints about the adulteration of texts are fairly frequent in early Christian literature. Christian texts, scriptural and nonscriptural, were no more immune than others from vicissitudes of unregulated transmission in handwritten copies. In some respects they were more vulnerable than ordinary texts, and not merely because Christian communities could not always command the most competent scribes. Although Christian writings generally aimed to express not individual viewpoints but the shared convictions and values of a group, members of the group who acted as editors and copyists must often have revised texts in accordance with their own perceptions. This temptation was stronger in connection with religious or philosophical texts than with others simply because more was at stake. A great deal of early Christian literature was composed for the purpose of advancing a particular viewpoint amid the conflicts of ideas and practices that repeatedly arose within and between Christian communities, and even documents that were not polemically conceived might nevertheless be polemically used. Any text was liable to emendation in the interest of making it more pointedly serviceable in a situation of theological controversy. [H. Y. Gamble, Books And Readers In The Early Church: A History Of Early Christian Texts, 1995, Yale University Press: New Haven & London, pp. 123-124.]