So my wife and I just played a game where I had an AutoScript Pilot Program in a remote server protected by a Tollbooth and two Matrix Analyzer's.  I had advanced the agenda once, she broke my Tollbooth, I then paid one credit per Matrix Analyzer and placed two more advancement tokens on ASPP.  Here is my question.  The rulebook, on page 14, says you can only score an agenda 1) before the beginning of your turn, or 2) after you have taken an action.  The book does not say "after you have used a click" would I be able to score ASPP?  Or does the effect on MA not count as an action.  Does the trace effect count as an action?  Or are the terms "click" and "action" mutually exchangable?  

As far as I understood that, action is what you as a player decide to do and clicks are a measure of time for actions. So some actions take just one click (make one cred) and thus are finished after one. Others take two or more clicks (purging virus counters), they are only completed after a time span of 2 or three clicks.

Click and action are different aspects of one game concept but technically far from identical.

As you can only score an agenda on the corp turn (as you stated, before the first and after each following action) you might find yourself having less than the 4 usual opportunities to score an agenda because you have to wait untilo an ACTION is completely resolved and that might take more than one click. No interruption in a multi-click action is possible.

ToneMastaG said:

Everything listed on the Corp Actions card are actions. Other things (such as using paid abilities) are not actions. The click symbol is a cost that you have to pay to use an action and some other abilities. 

ok so basically, there is no situation in which you can score an agenda on the runners turn, unless a card specifically says so.

Using a paid ability with a click cost (Melange Mining Corp, Private Security Force) IS an action, though.