Concepts of null and negative are only irrational in a sort of material accounting manner. That is, you can't owe people hydrogen in any physical way that I can think of (and hope not to find!). But we have created anti-hydrogen since 1995, being composed of the anti-particles of matter that makes up ordinary hydrogen.

Zero can be viewed simply as an absence. While it is true that nothing, as a state-position in space, does not exist, the concept of zero is still a rational quantity without which many fallacies are averted. For instance: how many lithium particles have I in this vacuum? If, in fact, there are none then I have zero lithium particles. This may seem pedantic, but it's important for other issues I will address shortly.

If I say that I have obtained zero grams of unobtainium, this is not to say that there is unobtainium physically available anywhere. In fact, by etymology we can see that unobtainium is unobtainable no matter what since if you found some it wouldn't be unobtainium. Unfortunately there are no examples of paradoxical elements such as this in the universe save the notes of certain engineers. This is my reductio ad absurdum for the formal fallacy Affirming the Consequent.

I think you are right to conjecture that the universe as a whole is made of something. This something seems to be, in a metaphorical sense, similar to a bitmap. As you noticed yourself there is no step down from what I assume you mean a transfinite state. You wrote infinity, though infinity is an operator used to mean "ever increasing in value" rather than an actual value. Infinity is something you use in relative terms, it's a destination rather than a position. Since we would have to cross vast amounts of infinity to get anywhere in life if the universe was mathematically concrete, movement would be impossible. Thus we come to deludedgod's Planck length, the very pixel dimension of matter.

Planck measurement is a difficult thing to absorb. It is a constant, but it varies depending on where it is used. If an atom is seated on the edge of a bit of warped space, part of the atom will have to work according to one Planck scale, while the other to a different one. Even so, space itself is conserved as the particles that make up the atom will only occupy spaces exactly so many plank lengths apart. We know this as the simplest possible solution for all known physical problems related to this matter.

Perhaps while I have your attention I can address something related. Though there is no integer decrement (step down) from a transfinite number, there are aleph steps up and down from different transfinite number. Similarly there is no such thing as a non-specific real decrement, since you cannot arbitrarily subtract a value from a real number and call it the same thing as the operation performed on another number. For example, the specificity of any real number (numbers with or without decimals) is greater OR lesser than the number of real numbers greater than the given value, but equal to the number of real numbers greater AND lesser than the number. The specificity of any given number makes the comparison between all of the integers and all of the reals look like child's play. This is just the tip of the iceberg as well; the set of imaginary numbers outmatches the reals by several magnitudes.

Thus, since we must agree that all sorts of complexity with influence to reality can be ultimately reduced to a collection of possibly strange numbers, the existence of any god with even basic complexity must have an origin. Since numbers are merely a concept and not a source in themselves it is impossible to have a self-sufficient god that predates everything.