The first part of this verse is the general reiteration of the truthfulness of the Biblical text, with the caveat that the Bible has had a history which has altered the "plain and pure." This sentiment parallels completely the removal of the "plain and precious" parts of the text, and should be seen in that light.
The comment that when the book left the "mouth of the Jew", meaning John, that it was "most precious and easy to the understanding of all men" is perhaps one of the most amazing statements to any who have ever tried to read and comprehend that text. It is currently anything but "easy to the understanding of all men." Does that mean that the text has been altered?
There is no evidence that the text has undergone anything other than the normal transmission process. The "easy to the understanding" must refer to the change in our culture and understanding which have altered our ability to understand the text. Perhaps it is no different than the new members of the modern church who are confused with the peculiar Mormon vocabulary and have to relearn what a Stake Center (heard as Steak?) might mean. Removed from the culture and time which produced it, it is somewhat more difficult to understand now.