Q:

Is there a transcription standard that separates unclear words from added words?

Right from the beginning I picked up the habit of adding [square brackets] round unclear or illegible words / letters in transcriptions and < angle brackets > round words / letters that I added myself to make the transcript clearer. However, I am totally unclear where I got this idea from and I have never found anyone else advocating this standard. 
As I wish to continue to distinguish the two cases, I intend to carry on doing it and will explain my convention in a note to the transcript. But I'd like to justify it if I can - so can anyone point me to a standard that distinguishes the two? Or justify why I shouldn't do so?
Example for clarity:
I would transcribe a will with an unclear signature from the testator thus:
"This is the Last Will and Testament of ... ... ... < signed > John [Dee]"
The word "< signed >" is not present in the original text, it simply indicates that the name following is a signature. "[Dee]" represents text that is unclear so it could be our old friend John Doe. 
Many books would transcribe this as 
"This is the Last Will and Testament of ... ... ... [signed] John [Dee]"
This would leave me to query whether the word "signed" is present in the original text (as it could be if I were transcribing what is already a transcription).
Grateful for any thought on this distinction.

A:

I was taught (by Steve Hobbs, one of the authors of: Lionel Munby, Steve Hobbs and Alan Crosby, Reading Tudor and Stuart Handwriting (British Association for Local History, 2002) ISBN 86077 237 4) to use [ ] to denote text that was not present in the original, and think this is the most widely used convention.
There seem to be a variety of ways to denote illegible or questionable text, including for example [MS.illegible], < possible transcription > and [question?ble]. 
I have also seen angle brackets used to differentiate printed and handwritten material in a document that contains both, and to denote material that was crossed-through in the original (although I suspect strike-through font is used more commonly now).
The Minnesota Historical Society has a set of rules for transcribing documents here, which uses [ ] to denote added or illegible text, and adds italics for 'commentary' by the transcriber.
Using these rules, I would transcribe your example as:  "This is the Last Will and Testament of ... ... ... [signed] John [D?e]"
I'll note that the University of Virginia Press and the authors have just released the Guide to Documentary Editing (free). It addresses in great depth the selection, description, and critical annotation of original documents and historical and literary texts, which includes the (large number) of conventions for transcription.

A:

There are a number of projects concerned, as you are, with an easy and efficient way of marking up the text of manuscripts to enable them to be interpreted as fully as possible without losing the original. Most of them are based upon defining a set of "tags". Many people will be familiar with "tags" as part of making an HTML page.
Your use of < > and [ ] represents the minimal set of tags. It works well for your purposes but cannot really be extended (because you will run out of unique characters) if you wanted to specify other possibilities such as "legible but misspelled" and "author's amendment" for example.
Most schemes designed for digital documents representing manuscripts use tags that resemble HTML and usually called SGML or XML (depending on their age). Your example of  "< signed > John [Dee]" might be marked up as  "<interpolated>signed</interpolated> <uncertain>Dee</uncertain>". 
You can find out more about manuscript markup at websites such as 

University of Virginia eText
Center and
TEI Manuscripts Special Interest
Group

There is no reason why you should not keep using your system, so long as there is no risk of any of your single characters used as tags having another meaning in your texts. If at any time you wanted to switch to a more elaborate scheme, a search and replace operation could automatically substitute any other tag form for each occurrence of yours.

