Structure of a paper: Development of a simulation approach
It depends on your target audience, but my inclination would be to say that unless you're specifically targeting an audience that would be interested in the detailed implementation (say, computer science), the means by which you implemented the theoretical model may not be sufficiently interesting to include in the main text.  With that in mind, I'd recommend the following structure:


Introduction
Methods


Theoretical Model


Reference to the appendix for implementation details

Use Cases

Results of use cases


Confirmation of model validity with use cases
Novel findings produced by the model

Conclusions
Appendix (or supplemental material, depending on the journal's requirements)


Details of implementation
Public location where source code will be available following publication



This structure comes with the caveat that I work in a field where models are valued for their ability to generate new findings, and are of lesser interest when they don't advance the state of knowledge within the field.  If your field is more interested in the implementation details you may want to go with your original layout and place the implementation description within the main text.

As for the other questions, I would describe the model in detail in the methods section, and compare the modelling approaches broadly in the introduction (with the bare minimum amount of detail to justify your new approach), and specifically in the methods, with an emphasis on why your approach addresses a weakness of the previous approach.