Oh Man. Only two days. As a first timer, I agree with the others, you will need to spend both days on the battlefield. Museums take up too much time. That being said, I would suggest one museum to stop at, the Seminary Ridge Museum (Lutheran Theological Seminary). Pay the extra fee and go stand up in the Cupola where Buford stood watching the battle on Day 1. That alone is worth the trip. There are many historic original buildings tied in with the battle you should see, but that should wait until a second visit.
Now, the others are suggesting what to see, I want to tell you WHERE TO EAT. In the 2 days you are there, you MUST stop and eat at the DOBBIN HOUSE INN and TAVERN, located at 89 Steinwehr Ave., right across from the National Cemetery. It is a stone building, the oldest surviving building in Gettysburg, built in 1776. It has been restored to its colonial appearance, and is now 2 restaurants, a tavern in the cellar, and fine dining upstairs. Eat at least once in the tavern. It is an amazing experience.