What long-term effects did the war have on issues such as civil rights, the power of the federal ...

The Civil War opened the door to many changes in the country. Slavery was abolished, but inequality between Black Americans and the rest of the populous remained for many years to come.

The 14th and 15th Amendments aimed to secure basic rights and voting rights, but enforcing them proved difficult in the face of resentment and resistance in the South, as discussed in the previous question posted.

The war also fundamentally altered the balance of power. The federal government emerged much stronger. Having successfully preserved the Union by force, it gained a precedent for asserting its authority over states' rights.

However, the Reconstruction era's failures also showed the limits of federal power. Despite the North winning the Civil War, they couldn't fully enforce the changes they envisioned in the South, particularly regarding racial equality.  The return of Southern states to Democratic control by white Democrats in the late 19th century weakened Reconstruction gains and left a legacy of racial violence and segregation. 

Other questions that remained to be answered were the following:

1)  What was the relationship between the former Confederate states and the federal Union?

2)  What should be the position of the newly-freed slaves? What responsibility did the government have to extend basic rights to them? Which rights?

3)  How should the Southern economy be converted from one based on slave labor to one based on free labor?