Ubuntu/Fedora (to mention a few ones) is composed for several applications or programs dedicated each one to a specific task, but I've got a few questions:
A little bit of google-fu would have helped here. Not that you are not right to ask: it's perfectly fine. But the very first thing you should be able to do is to find information yourself, read the doc, and so on.
What you describes is distro specific. For instance for Debian and derivatives (such as ubuntu) apt-get source [package] is what you need (see here for instance or man apt-get source or search engine). This way, one can edit the sources of the versions of the programs that are used in the distro.
If what you want is to contribute to an open source project directly, you shouldn't use distro specific sources but the upstream sources usually managed by a version control system (quick how-to for git and github, assumes that you already know what we are talking about).
There is nowhere to start from. There aren't good practices. But if I were to forge a new distro, I would begin by wondering why I want to create a new one. Isn't there a distro out there that would fit my needs? If not, is there one that is close enough to ask its maintainers whether they are interested by a new contributor?
It depends on a lot of things. But usually for compiled languages, a
./configure --prefix=[install directory]
make
make install
should do it, but again, read the doc. Packages are usually release with INSTALL or README files, read them. And again, your favorite search engine should give you all the details about how and what to do to get your system ready or to solve common problems (99.99% of them are common).
for getting source code you can install linux-source or linux-source-XX such as edit,update,compile and for create new distro based on ubuntu you can use constructor tools
