Can you add nouns/adjectives/articles in a direct quotation in Chicago MoS keeping the message intact? I need to quote something from an author. 


  ... during an economic downturn, it is no easier to find a job in a region with lower prevailing unemployment than in one with a higher unemployment rate.


As you can see, the sentence is a bit awkward as it does not have a parallel structure. I am wondering if in my quotation, I can edit it without changing the meaning. Are the following additions acceptable? See the following edit.


  "... during an economic downturn, it is no easier to find a job in a region with a lower prevailing unemployment rate than in one with a higher prevailing unemployment rate." 


Mine has a parallel structure. My guide, the Chicago Manual of Style does not say anything about putting in such words to improve clarity. It does however allow changing spelling, punctuation, and capitalization.
You are allowed to add parenthetic words to a quote, so long as your additions are consistent with what the original author was trying to say.  The standard method is to use square parentheses to show an addition or replacement you have made to the quote.  Thus, you can write your altered quote like this:


  "... during an economic downturn, it is no easier to find a job in a region with [a] lower prevailing unemployment [rate] than in one with a higher [prevailing] unemployment rate." 


By putting the additional words in square parentheses you indicate that you have added them to the original quote.  The reader will see that the original author only referred to "unemployment" rather than the "unemployment rate" in the first instance, you have added the additional word.

I tend to agree with other commentators here that this addition is probably unnecessary.  If you particularly want to frame things differently than the quotation, I would recommend paraphrasing here, instead of quotation.  In any case, the above is how you make additions/alterations to a quote if you want to do that.