You are very close to the truth, but you took a right hand turn instead of a left hand turn...your paper states:
"There is no experimental evidence that clocks measure time. It is convenient to replace the concept of time with the numerical order of material change. This view corresponds more adequately to the physical world and resolves Zeno problems of motion."
But what clocks measure is what defines time. In fact, all objects in the universe are clocks since there is a fossil time record in how every object evolved. Clocks are simply objects that have a very regular action called a tick rate, but the earth is also a clock in the fossil layers of its geology. We can tell time with any object, but clocks are especially useful.
You replace the word time with a words numerical order of material change, which sounds a little bit like replacing continuous time with the discrete time delays of matter change. In denying continuous time, you accept discrete time delays, but call it a "numerical order of material change."
There are actually many different ways to describe how the universe really works but you really should not simply redefine time with new words for time. This can be really confusing since your main thesis is really about the vacuum energy of space, not time. Another paper states:
"Starting from the above fundamental considerations, we have already proposed [7] a novel model of Quantum Vacuum consisting of a granular structure of the universal space, similar to that assumed, for example, in many version of loop quantum gravity, but conceptually very different and based on the conception of a physical 3D space composed by energetic packages having the size of Planck volume."
So you redefine continuous space with a discrete granular structure that you call the quantum vacuum of universal space. You even have a particle for that quantum vacuum that defines all matter...go figure. However, nowhere do you use the term aether.
In other words, you have an aether theory in every possible way except the word. These kind of euphemisms are used in most aether papers since there is a strong prejudice against the notion of an aether that fills space. Your quantum vacuum is a classic example of an aether that fills space.
You have not yet gotten to the pressure-less dusts or quantum fluids of others, but I see the outline of those issues in some of your various papers. There are numerous pathologies that you need to address that you have not yet addressed. You work very hard explaining things that already have explanations, like gravity. You should focus more on explaining things that have no explanations, like black holes.
Thus your approach is to fill space with aether called quantum vacuum and to replace time with sequences of discrete events. What happens at the event horizon of a black hole? What is the entropy of a black hole? Does your quantum vacuum explain why the CMB is so uniform? Are the speed of light, Planck's, and fine structure truly constant for all time?
Predict something that we do not already know and then measure it and verify your prediction...