Currently when you move a planet around it's locked to a flat plane in line with the largest body in the system. The ability to change this plane and the base object will come in a future update.
In the meantime, like Laura suggests, use the orbital element adjustments to change the inclination.
I'm not sure why it would take so long to close.
Have you installed the latest update (2.0.6)? Does either problem still happen?
Some simulations do take a long time to load (like constellations), but most do not. What simulation is taking a long time?