Um... that is a real head-scratcher. Have you ever heard of DNA? All of the information needed to shape the organism is right there. Instead of memorizing the content of anti-science sites like Answers in Genesis and its ilk, how about reading up a bit on genetics, biochemistry, embryogenesis, etc.?
As for species transition—if evolution is true, then some species currently existing would necessarily be defined as precursors of other species also currently in existence. And by the laws of probability, some of the precursors would have to be very close to their successors in the evolutionary trajectory, while others would be not so close.
Obviously, you did not read my previous posts. Since evolution is a continuous process, every organism is, by definition, a transition organism. And evolution takes place a few mutations at a time, so it takes millenia to see distinct changes in a long-living species like humans. Nevertheless, your genome contains mutations not present in either of your parent's genomes, and none of your chromosomes (except the X and Y) match any of your parent's chromosomes. With that kind of genetic mix up at every generation, you don't have to be a rocket scientist to understand that the genetic composition of a species after 100 generations will be different than its genetic composition right now. And after 1,000 generations, it will be even more different, and at some point many generations hence, it will not be the same species any more.
We only have some species which can be claimed to be on the same line of evolution as others, but only distantly related—and even this often seems a stretch of logic.
Um... science does not progress through logical exercises. The only criterion that matters in science is measurable and observable evidence. It is not logic that tells us that the genomes of humans and chimpanzees are only about 5% different--this determination was made by actually comparing the two genomes, chromosome for chromosome, gene sequence for gene sequence. These days, we use phylogenetic trees a lot for mapping evolutionary relationships. You might try reading up about them sometime.
Do not confuse your own ignorance of biology for any real gaps of knowledge within the field. You'd do well to assume that whatever you don't know, someone not only knows, but is actively researching that topic. Also, just because something isn't known yet does not mean that the knowledge does not exist or is unknowable--it just means that it is merely waiting to be discovered.
If you take a course in genetics at any university, you’ll find that exams require the ability to describe the processes of dna replication and rna transcription, the process of translation into proteins.
In other courses of biology and biochemistry, you’ll need to know about how carbohydrates and lipids are processed and sometimes synthesized.
But there are no exam questions that require a description of how particular genetic sequences produce particular morphological shape on the macro level. Knowledge of how this is achieved is totally absent in the field of molecular biology.