Jennifer,
When did you pot this tree in the pot it is in now?
If you repot it now. Lift out of soil and clean off roots. This way you will be able to check for possible discoloration (probably will not be). Just something I do whenever repotting.
Choose a pot to put it in that will house the roots to no less than 1" - 1 1/2" on either side of widest part of root (caudex). You can raise it at this time by say 1" or so.
I like to only raise to the widest part, as I prefer a upside down " ^ " shape to finished appearance. This is my preference.
Pruning can be done in the spring, if desired.
Rick