Code cleanup: Follow up PR #986 by replace utils.instance_from_dict()++ with JStore

[jesper-friis]

The Python interface to JStore implemented in PR #986 makes it possible to remove a lot of duplicated code related to the dict-representation of instances and to convert between different dict-representations.

The main benefits are (i) consistency due to a single source of implementation and (ii) increased maintainability due to a single source and reduced code size.