You are conflating things of different kinds. In addition, I think you may be making a category mistake, although I'm not certain of this.
MikTeX and TeX Live are distributions of TeX in the sense of 'everything' or, more accurately 'most of it'. If you install them, you get TeX, LuaTeX, ConTeXt, XeTeX, LaTeX, a bunch of packages, scripts, additional tools etc.
TeX, pdfTeX, LuaTeX, XeTeX and ConTeXt are engines. These turn
.tex files into processed documents: DVI or PDF.
plain, LaTeX and ConTeXt are formats. They are built up from the primitives provided by core TeX. If people say they are using TeX, as opposed to LaTeX, they usually mean they are using the plain format. But this is still a format built on top of the core, just as the other formats are.
This list is not comprehensive. There are many formats and you can make your own quite easily. But these are probably the best known, at least in the West.
Core TeX and the plain format are described in The TeX Book. LaTeX is described in Lamport's book and in the documentation provided with the format. Using the LaTeX format, as I understand it, is equivalent to loading
latex.ltx. Using plain is equivalent to loading a file containing the macros defined by that format.
ConTeXt is both an engine and a format.
Otherwise, you have
A format is just a pre-compiled bunch of code which you could load, but it would be slower and less convenient.
Many of the above binaries are binaries-by-name, by which I mean that two different names invoke the same binary, whose behaviour depends on the invoking name.
lrwxrwxrwx 1 texlive texlive 6 Tach 25 2016 ../bin/x86_64-linux/latex -> pdftex*
lrwxrwxrwx 1 texlive texlive 6 Tach 25 2016 ../bin/x86_64-linux/lualatex -> luatex*
-rwxr-xr-x 1 texlive texlive 8.4M Ebr 2 18:10 ../bin/x86_64-linux/luatex*
lrwxrwxrwx 1 texlive texlive 6 Tach 25 2016 ../bin/x86_64-linux/pdflatex -> pdftex*
-rwxr-xr-x 1 texlive texlive 2.1M Maw 26 23:02 ../bin/x86_64-linux/pdftex*
-rwxr-xr-x 1 texlive texlive 371K Maw 21 21:47 ../bin/x86_64-linux/tex*
lrwxrwxrwx 1 texlive texlive 5 Tach 25 2016 ../bin/x86_64-linux/xelatex -> xetex*
-rwxr-xr-x 1 texlive texlive 23M Ebr 2 18:10 ../bin/x86_64-linux/xetex*
As you can see, invoking
pdflatex invokes the same binary as does
pdftex. The difference is that the former results in the use of an option specifying the LaTeX format.
As was said in answer to your previous question, The TeX Book and the source code for TeX are the place to look. The rest is just elaboration.
The LaTeX 3 project concerns development of the third major version of the LaTeX format. Currently, the version is 2e, though some parts of the L3 project can currently be used on top of 2e. Like 2.09 and 2e and (presumably) version 1, this is 'just' a format on top of TeX. It is not different from TeX in the sense of being an alternative. It is different from TeX in the same way that a house is different from its foundations.
The CTAN page you linked includes links to some extensions e.g. eTeX and pdfTeX. So you could look at e.g. https://tug.org/svn/pdftex/branches/stable, but then you are looking at extended versions and not a bare-bones version i.e. if you want just the core, look at the source for the core. If you want to see how it has been re-implemented and extended, look at the source for eTeX or pdfTeX or LuaTeX or whatever.