Let's try taking this from another direction. StratThinker, you clearly accept that genetic mutation and natural selection produces variation within species, regardless of how we're defining the word "species". You've already said as much. So, explain to me:

- Exactly how we're defining "species" here, and where we're drawing the line between a "species" and a "kind".

- How that line prevents the same mechanisms of genetic mutation and natural selection from applying anywhere higher in the hierarchy. We'll set aside the other mechanisms involved in evolution, because you don't seem to be aware of them.

- Your alternative explanation for the apparent genetic and fossil lineages that evolution is used to explain.

1) I draw the line between a species, kind and a sub-species as this:
a) A group of animals are in the same species if and only if most of them can produce fertile offspring with each other. (Thus if group A of animals can produce fertile offspring with other members of group A, and similarly for group B, but group A cannot produce fertile offspring with group B, then group A and B are of different species). Note this a simplest definition and does not consider that you may have group A can reproduce with group B, and group B can reproduce with group C, but A cannot reproduce with C.
b) A species can split into sub-populations which due to variations over time, the members of the sub-populations can no longer produce fertile offspring, thus one species can become multiple sub-species. This is called speciation.
c) What I would call a "Kind" is one of original species that God created which could not reproduce with each other at all, I would also use it to encompasses all of the daughter species of the original species. It is probably impossible to fully know what are the original kinds (please read carefully), but it is possible to put some limits on what they were. If two animals can produce any offspring (even an infertile one) via natural means, then they are of the same kind and their species are of the same kind. For example Lions and Tigers are of the same kind. If species A and species B are of the same kind, and species B and species C are of the same kind, then species A and C are of the same kind even if no member of A can reproduce with members of C at all (i.e. the kind relation is a transitive relation, it is also reflexive and symmetric)

Note the last statement makes the idea of "kind" falsifiable (together with the fact that the Bible says that there are more than one kind of animal). If according it, we can show that all animals are of one kind, then we have disproven the Bible.

2) All animals, bacteria, plants, ect that ever lived are subject to natural selection and mutations. What do you mean by "higher in the hierarchy"? According to the creationist model, the highest in the hierarchy is the kinds.

Are you asking "why couldn't all of these variations given rise to all known species starting at one species, why do these changes 'stop'"? The changes do not stop. Natural selection decreases genetic diversity but increases fitness. Mutations increase diversity but usually decrease fitness. If you have too intense natural selection, then you get genetic uniformity. If you have too little natural selection, then risk a gradual increase in multiple recessive harmful mutations per individual, up to the point where if almost any two random individuals reproduce, their offspring will have a pair recessive harmful mutations. Thus it is not that the changes stop, it is that they are not necessarily sufficient to produce the tree of life.

I am very tired, and I must work tomorrow. So I can't complete this now.