The other website is still around at http://www.civilwarsignals.org/pages/tele/tele.html
That site contains several quotes by Walt Mathers. Walt was an expert on Civil War telegraphy. Alas, Walt passed away a few years ago. He describes a dot code used on telegraphs on that webpage.
I did have some correspondence with him before he passed about the USMRR Dot code. Unfortunately, his answers to my questions were not very clear. Here is an excerpt from a message I received from him. Note that the 3rd, 4th and 5th paragraph describe a dot code, despite him saying that a dot code wasn't used in the first paragraph.
"To the best of my knowledge, neither the USMT or their Confederate counterpart used a two-element dot code. American Morse system, of four elements, was used on land lines. While the 1852 Berlin code, of two elements, was used on the 1858 trans-Atlantic cable, and the Bain code, of two elements, was absorbed by a successful law suit brought about by Morse, the land-line, or Morse code (actually invented by Alfred Vail but that's another story), was used.
The Union army's chief signal officer, Albert James Myer, who had been a Bain two-element operator on the NY line as a youngster, developed a simple code that could be used on an electric telegraph magnet using single blows to represent a dot, i.e. a single blow representing the numeral "one" ... and two quick blows on the sending instrument (to signify a "two".
This code, which superseded Myer's original four-element code of numerals (one through four with five being used to end a word, two for a sentence and three to finish off a message), could be used with flag and torch or as a homographic code of using one's limbs.
So, instead of using dots, dash, extended (or sustained) dashes and spaces between dots such as the letters "Oh" "Rah" or Cee" with the Morse system, a signal operator could use combinations of single or couplet blows of dots upon the sending instrument's anvil.
Neither US or CS landline telegraphers have ever been documented as using a dot code in the field. Did others, such as army signalists use it in a pinch on electric lines? We just don't know. If documentation does surface we'll let you know. Re-enactors do effectively use it to good effect to communicate over their distant event wires."
I found this document on another website, but I did not record where I found it. It contains some additional information on dot code and operating procedures used by the telegraphers.
Myer's system is described in this document. http://www.civilwarsignals.org/pdf/lgmanualofsignals.pdf It seems to apply primarily to flag and torch signals, but he does briefly mention electrical signaling in the document.
From this message traffic it appears that using dot code on electrical telegraph was used by re-enactor telegraphers, but perhaps not very likely by actual civil war telegraphers.
