Not sure if I got your goal correctly but based on the examples you gave the following approach might work.
CC = {}
for step in range(len(Nodes['time'])):
for key in CoordComboSort.keys():
CC[Nodes['time'][step]] = {key : CoordComboSort[key][step] for key in CoordComboSort.keys()}
For your input, the output will be like this:
{'A': {0: (1, 4, 5), 0.001: (4, 6, 8)}, 'B': {0: (1, 7, 4), 0.001: (3, 8, 6)}}
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solved Updating a Dictionary within Python