Thoughts from someone who has lived his entire life in DC AND has been in the tour business for 40 years:
If you haven't gotten them yet you need to get tickets for Ford's Theater and Downtown ( National Mall) Air and Space museum. Only about 1/3 of the museum is open to the public but that's still a lot. There are several variations on Ford's tour tickets ranging from a walk through to Museum, Ranger Talk and Peterson House which would take an hour and half. Wok and Roll/Mary Surratt House is a short walk from Ford's. Rangers can tell you how to get there.
Washington Monument tickets are also nice if you can get them.
https://www.recreation.gov/ticket/234635/ticket/193
I'm not sure when and where you will have a car. There is parking at Lincoln Cottage. Finding it is tricky however so use GPS.
Ft Stevens is not too far away. It's basically a small city park with signage and a cannon. There is a nearby cemetery on Georgia Avenue. I lived in the area as a small child and played in the park.
Not sure what the parking situation is at African American CW Memorial. It is above a metro station. Contact them for more info.
https://afroamcivilwar.org/
B&O Museum had parking last time I was there. Babe Ruth House didn't. It's a short walk from Oriole ballpark.
North Point Battlefield is in the eastern suburb of Dundalk. I seem to recall it as a park in an urban setting. Again GPS is helpful
Visit Ft McHenry first. The Rangers there can give you advice about visiting North Point and what is actually there to see.
There is no free parking in downtown DC or Baltimore.
Your itinerary is ambitious. Prioritize what you want to see.
To visit Ball's Bluff will require some hiking in a hilly wooded area.
I'd suggest taking routes 50 or 7 to Winchester and making some stops at CW marker sites.
Crime is in fact a problem in DC but not in the Federal areas and not in the downtown area during daytime. Sadly the area around (Gen Thomas) Circle is an area that has seen an increase in carjackings and street robberies. Crime has seeped into residential areas that were generally considered safe and that has resulted in a bill being passed and signed this week to take stronger anti crime measures. In addition two city council members are facing recall votes over crime.
None of this should affect your visit.