My opinion is based much more on an idealization of the process of refereeing, rather
than the actual process itself, so this opinion may have little worth. It appears to me
to have much common sense, so I will share it anyway. (This may all be in whatever
procedure or policy manual for referees the journal has.)
The goal of the process is to have someone spend resources putting ink to paper. There
are other goals, such as scientific progress, but let us take the economic viewpoint.
The representative of the people spending these resources is the editorial team. The team
is involved in the process of deciding how to arrange the ink. Your questions and
eventual evaluation are key in this decision. I suggest that you send a dated letter
(or email) which they can easily extract and forward to the author. In short, they need
to be actively involved in the forwarding of such questions.
There are several techniques you can use which ease the process. For one, leave any
reference to yourself out of the letter, so the editorial team can put such in if needed.
If you leave whitespace between the questions, you encourage the answerer to fit their
answer in that space. Having the answerer meet the challenge of giving a concise answer
usually promotes proper answering, and adds value to the process.
Nowadays, many people use a computer to search for a substring. Even so, use every
appropriate landmark to help locate the relevant text, as well as an appropriate string,
e.g. "Near the end of your second section, just before Lemma C, you have the phrase '...'.
What were you thinking when you included that phrase?" .
With the letter to the author, include remarks intended only for the editorial team,
saying what will happen if the questions get answered promptly, e.g. your referee report
will come six weeks earlier, or you anticipate a particular problem which may evaporate
if the right answers come, otherwise you will recommend the problem be fixed. If the
editorial team knows explicitly how passing the letter on will benefit them, they will
be more motivated to pass it on and save time.
Arrange it so that you only need to send two or three such letters at most. This will
involve phrasing your questions properly and accumulating them so that this part of
the process is economically advantageous. Also, while becoming a referee,
make sure you understand and agree with enough of the editorial process, so
that it will allow timely transmission of such questions and answers.
Gerhard "Ask Me About System Design" Paseman, 2011.01.02