I disagree. If you read William Lane Craig's writings on the kalam cosmological argument, he says that God existed outside of time, and in creating time and space entered time. There's no logical inconsistency there. What that means is that God need not have a beginning.
(As an aside: Christians, of course, believe God is Trinity. That means that God the Father is outside of time, and God the Son is within time. So God is both inside of time and outside of time.)
You're also presuming that God has to act within the physical laws of the universe. Christians believe in the uniformity of natural causes within an open system. In other words, we do accept that the universe behaves according to physical laws, however, these laws are subject to reordering by God: hence why Jesus could rise from the dead. That is not an impossibility. Look at developments in quantum physics: at a quantum level, electrons and various components of atoms do not act according to any discernible laws. So what?
So what indeed? It's interesting that at first you stand by the Kalam argument, the core of which stands on rigid causality (whatever begins has a cause, therefore the universe too must have a "prime mover") and THEN you call on quantum physics to explain how Jesus could rise from the dead. The only problem is that at the level of quantum physics the exact causality which you expect at the formation of the universe breaks down. Again, the cake. You can't have it both ways.
Of course quantum mechanics are a great mystery to us at this time, and maybe we will understand it better in the future or we may not. It is my hope that as we have come to understand lightning, we will, in time understand that matter REALLY is. What I don't see the need of, is to full the "black spots" of of our under standing with imaginary creatures like the cartographers of old did by drawing dragons on the undiscovered parts of their maps. We just need to accept them for what they are: black spots
As to how precisely the spiritual world interacts with the physical world: sure, there are limits on what we can know as human beings. That doesn't make the concept of God affecting stuff in the physical world *improbable* per se, it simply means that we don't know how precisely that occurs. Isn't that exactly what we should expect when it comes to God? He is infinite, we are finite: there are some things we should not expect to understand, especially as we operate in the physical world.
First, we would need to see something that would actually INDICATE there is something to look for, like this "spiritual" world you mention. Otherwise this is, and always will be another quest for "El Dorado". Now, if you said that we should instead focus on understanding what what exactly "Matter" is, what's it really made of, and how it may transform into its various forms, then yes, I would fully agree. The guys at CERN are doing their best.
I am a former militant atheist who converted to Christianity after a series of supernatural events in 2008, climaxing in one particular experience which has absolutely changed my life. As a result of that encounter I went instantly from hardcore atheist to believer. I can say without the shadow of a doubt that God is real and that spirits (good and evil) can affect the physical world because I have witnessed that with my own eyes. You can believe me or not but when we start having an abstract conversation about how exactly God or evil spirits affect the physical world I just find it a moot point.
As a former atheist, you should know that human perception is FAR from being an accurate reading of reality Everything you see, hear, taste and feel, go through various switches (e.g. receptors, nerves) all of which are far from fool-proof before reaching your brain. When your brain receives the signals it still has to interpret them and then it still has to make sense of what that thing is. It works MOST of the time.
Then, there are circumstances when the system works funny, quirks or even fails. When someone takes hallucinogenics, they go on a "trip" but they don't actually visit all the magical places they see, in reality, they're sitting on a couch staring blankly into space. It's the chemicals and cross-firing receptors in their brains that give them the experience. Even without the use of hallucinogenics, people may "see" things that actually aren't there. These are so common that just in my family there were two "sightings" of "supernatural" beings (one hilarious and one deeply tragic), and I have no reason to doubt the sincereness of these claims. Being aware of the specific circumstances though, I am not surprised they happened.
Even large groups of people can be deceived, just look at the "Miracle of the Sun" where tens of thousands apparently saw the sun zig-zag across the sky, and some other crazy things. I think we can empirically state that the Sun did not zig-zag anyhere (because if it did, It would have scorched Earth and the rest of the Solar System). All this is a proof of is how human perception is inaccurate and how the psyche can work in incredibly strange ways.
EDIT: That Trinity thing though, wow.... It's so hilariously convoluted that Christians themselves never got to understand it, let alone agree of it (see why a good deal of schisms happened). On this, I can somewhat agree with some Muslims when they claim Christians are actually polytheists 