Usually the best way to brainstorm is to at least understand what is known. Saves time falling down lots of holes that everyone else has already done especially on something so complex.
So lets see if you are at least ready to start and ask two simple questions
1.) What physics framework are you going to use to try and start understanding the whole universe?
2.) Do you know the problems and dependencies of that framework and where it currently breaks down?
You have given me hope with your rephrasing to ideas ... that is a very good start.
There is no framework we have that doesn't have breakdowns so you usually need to start with one and try and extend it. The current one most go for is GR and try to bind QM into it which is the big ticket item it doesn't cover. The scary alternative is to build your own framework but it is a lot of work and most lack the disciplines to attempt it.
For the record: The usual answer on here is classical physics and it doesn't break down and which point I roll around laughing, as some school teacher did a really good job. So if someone doesn't realize that classical physics doesn't even work with what we already know, how do they really expect to go further.
There is a semi decent version nicely labelled "The never-ending conundrums of classical physics" here if you need a refresher on classical physics breakpoints (
http://arstechnica.com/science/2014/08/the-never-ending-conundrums-of-classical-physics/). It leaves out all the QM ones because that would require a book on its own and most layman would never understand the problems presented.
The truth statement here is:
Since we know that classical physics is not correct, we might agree that it’s not a fundamental theory. However, neither is special relativity, which explains neither gravity nor reality at small scales, for which we need, respectively, general relativity and quantum mechanics. However, since these two magnificent accomplishments of modern physics have not yet been reconciled into a unified theory of quantum gravity, neither of them is really fundamental either. Today we have an assortment of models, each of which does remarkably well within its scale of length or energy but can not be applied outside that realm.
That is a tricky staring point for anyone and you need to know it before beginning ... most crackpots don't even try and understand that much.
