Harpers Ferry isn't far from my home. The Capitol Limited stops there, but automobiles aren't permitted in town, so you might be better off if you detrain in Martinsburg, WV. I think you can rent a car there. Not many (if any) places to stay in Harpers Ferry, but there are several in Shepherdstown (home of Shepherd College), Martinsburg (location of a famous Stonewall Jackson raid on the B&O RR), Hagerstown MD, and other nearby towns. The Antietam battlefield is just up the road at Sharpsburg, MD. Gettysburg is an easy drive of about an hour, and the advance and retreat from Gettysburg passed through Hagerstown and Williamsport, MD. South of Martinsburg you will find Winchester, New Market, and other Civil War sites. The C&O Canal runs right through the area, on the north side of the Potomac River.
If the Civil War is your thing, this is the area to visit. By the way, Gettysburg tends to be crowded. Visitors have been known to ask how the soldiers managed to fight a battle with all those monuments in the way. Antietam is much less so (except on July 4 and the battle anniversary in September).