I have little to no personal experience with writing extensive stories, however I would recommend you try putting the ideas you have right now and try to write a brief story using some of the ideas (not all) that you plan on implementing to the full thing, just enough for you to have a good feel of how's its going to work out.
Right now the only thing I'm worried about is the the possibility of characters with almost unlimited power (the level 5's) becoming unwieldy in the story telling, particularly time travel ones.
My word isn't expert wisdom by any sense, it's just suggestions. There's probably other users here that could give you much more informed advice and critique.