"The Schedule D seems to only be allowing 2 transactions."

You can make as many entries on Sch D as you'd like, once youve completed one, just keep hitting the Enter button or Page Down button to go down to the entry table. 

When those first 2 fields are empty it only looks like you can make 2 entries, but once youve got those first 2 completed, you're allowed to move forward and fill out more.