So the real MacGuffin in Mass Effect was the fact that Normandy was on a "shakedown run".
Not really. The Normandy shakedown run was for the Beacon, whose nature was important to its function in the plot.
Not all stories have MacGuffins. The closest ME1 has is probably the Cypher- which functions as a black box plot device of vagueness which has one use and one use only to decipher the Beacon by mumbo-jumbo, and then never matters again (even though it should matter quite alot). The Cypher could have been any interchangeable macguffin and made as much sense, which is why it's closer to being the macguffin.
MacGuffins usually qualify when 'what' the MacGuffin is isn't what's important to the story. The archetype is the locked briefcase- what's inside the briefcase doesn't matter, as long as people come into conflict over it. If you can go the story without actually saying what's in the briefcase, or could trade it out easily for the same effect, it's probably a macguffin.
In ME, the most common macguffins were 'data.' What sort of data is almost always pure technobabble of situational context, but having the 'data' was important. The cure data in Mordin's loyalty mission, for example- it's a macguffin because the story didn't really care what was inside it or even if it existed. It could have been useful- it could have been junk data. The conflict would have been the same.