Henry, actually the dispatch from Davis, of which a copy was also issued to general Whiting, is in Army Official Records series 1, volume 51, part 2 (not part 1, as I indicated), on page 829. A dispatch on the next page, dated the same day, and sent by Whiting indicates that Whiting instigated the president's action, though Whiting did not wish to be involved in any confrontation with Lynch.
My copy of the ORN series 2, volume 3, does include the pages that you are missing, so, if you want me to scan them and send them along, let me know, and I will gladly do it. They are mainly political dispatches, sent by John Slidell and J.M. Mason, etc.
Referring back to the presidential dispatch, I feel that it is the first time I have ever seen one sent by the president, and ordering the removal of a Naval station commander. It seems to be quite a forceful directive, and Lynch must have really been a "bad boy," to get such a dispatch, directly from the president.