I don't know what to do with this! Help!

I am going to disagree with Jody.  Adding in the commas, you can break this into separate thoughts.  

Phrase one:

"My goal is to pursue a Master's degree with an emphasis on Russian and Eastern European history..."

Phrase two:

"...by examining Russian actions as viewed from their national interests and identity..."

Phrase three:

"...thereby assist in changing misconceptions about modern and Soviet Russia."

Place them with what they actually go with.

"My goal is to pursue a Master's degree with an emphasis on Russian and Eastern European history [to] assist in changing misconceptions about modern and Soviet Russia, by examining Russian actions as viewed from their national interests and identity."

I think the issue is confusion as to which word modifies which phrase.

I'll have to disagree with Jody as well.  Because the commas would separate the three sections into separate thoughts, examining and assist do not have to match.  Indeed, I'd say the middle phrase is essentially an interjection, and the first and last would have to match form, which they do.  E.G. "My goal is to pursue . . . and assist . . . by examining . . ."

Because of all the disagreement with my original answer, I feel an explanation is in order.  It is poorly written, and for that, I apologize.

The first part of my answer (Since examining ends in -ing, assist needs to as well) is in response to the question about the faulty parallelism.  The Purdue Online Writing Lab explains parallel structure, and provides examples.

I hadn't meant to suggest that a comma be added as well as changing assist to assisting.  But that is what my answer implies.  Making the changes that I suggested, the sentence wouldn't read well.  I agree with Rik's answer.  The sentence needs some rearranging.