Not perfect at all, but as you can't control the space at the end of the question, perhaps you can add a negative vspace before the beginning of each question. Perhaps this will need some adjustments before the first question, however.

\def\AMCbeginQuestion#1#2{\vspace*{-0.1cm}\par\noindent{\bf Question #1} #2\hspace*{0.0em}}

You can also try the attached package (using \usepackage{qvspace} after \usepackage{automultiplechoice}, with the qvspace.sty file in the same directory as the source file), which rewrites the question environment, so that you can modify the vertical space after the questions, which have the following default values :

\AMCafterQbloc=3ex

when using the box package option, and

\AMCafterQ=0pt

without the box option.
If you find this rewrite useful, I will incorporate it to the development version of AMC.

Wow, I tried the first tip which worked well. Then I tried your .sty sheet which worked amazingly well and will be extremely useful for making streamlined tests. Thank you.

As I was experimenting with this, I noticed that with the box option, my "short answer" type question (using "\AMCOpen") still has more space than the rest of the questions. But, when I take away the box package option, everything behaves great including the \AMCOpen questions; there is no extra white space. To replicate the issue, all that is needed is to remove the box package option from the code below to see that it works fine without the box option. It appears that the box option puts some extra space on this type of question or something. Any ideas on how to get this to work with the box package option? The question type that has extra white space is written like:

\element{general}{
  \begin{question}{Yaounde} 
  What is the capital city of Cameroon?
  \AMCOpen{lineup=true,hspace=0.1mm,boxmargin=0.1ex,Treserved=Cam}{\wrongchoice[N]{N}\scoring{1}\correctchoice[Y]{Y}\scoring{2}} 
\end{question}
}

Complete code is attached.

This should be a little better with this new version of qvspace...

Great! That works perfectly.

This patch is included in AMC development version since revision r1351, but I changed the names of the dimensions a little for the sake of consistency with other old dimension names: they are \AMCinterIquest and \AMCinterBquest instead of \AMCafterQ and \AMCafterQbloc.

As I was experimenting, I found that there is a large inconsistent gap of white space if there is a "choicescustom" question followed by an "\AMCOpen" question. The gap is actually after the "\AMCOpen" question but it only seems to appear if there is a "choicescustom" question before it. I am not sure if this is helpful but I did want to point it out just in case. Then, if the "box" option is removed, it appears that the "choicescustom" questions also appear in a very strange way.

It happens in this instance:

\element{general}{

\begin{question}{id2}
\begin{choicescustom}[o]
        \wrongchoice[T]{}
        \correctchoice[F]{}
\end{choicescustom}
This is a True or False question.

\end{question}
}

\element{general}{
  \begin{question}{Yaounde} 
  What is the capital city of Cameroon?
  \AMCOpen{lineup=true,hspace=0.1mm,boxmargin=0.1ex,Treserved=Cam}{\wrongchoice[>]{>}\scoring{1}\correctchoice[<]{<}\scoring{2}} 
\end{question}
}

I have attached the full source code and removed the shuffle option to shows this.

I'm not sure this comes from the choicescustom before. Can you try removing the blank line just before the following question environment (question id3)?

Yes that did it...sorry about my oversight.

I am not planning on using it without the box option...but when I do take the box package option out, it still looks like the choicescustom question type is still noticeably misaligned.

Where exactly ?

With the box user package removed, whenever there is a question after a "choicescustom" question, with the settings I have, this question is written on top of the previous question. Although the other types of questions seem to be behaving properly with my settings. Of course this very well could be something on my end as well but if it is I cannot see it (and there is no problem with the same exact code using the box option and a similar spacing setting (\AMCafterQbloc=1.0ex). I have attached a pdf to show what is happening along with the source tex file (and I am using the latest qvspace.sty file that was previously uploaded).

Thanks to the instructions on the wiki I was able to build AMC from the repository and I now have v.1.1.1315 (svn:1361). I was able to duplicate the same issue using the new \AMCinterIquest option. So I have attached everything from the last post again using the new version and new verbage (not the qvspace.sty).