Issue with Homebrew when trying to parallelly install Python 3.x
brew doctor spits out possible sources of error in your setup (see a description of some errors and reasons for which they are triggered on the Homebrew Github page, like this). If you aren't running into issues with your setup, you can usually ignore the messages (they're there to help Homebrew maintainers to solve issues, should you have them). 

With this in mind, I think you can ignore the messages related to header files and .pc files from Jack. If you want to clear these ones, you can remove your current installation and brew install jack, which will house all of those files in "Homebrew-approved" locations. 

As far as the Python issues, it looks like you installed Python from a package downloaded from python.org. This resulted in your PATH being modified (either by you via their instruction, or as part of the install script) with a line in your .bash_profile. When you type python at the command line, the system will execute whatever version of Python it finds first in the PATH. In your case, it's the 2.7 version in /Library/Frameworks/. You can uninstall that version using the instructions here, replacing instances of 3.x with 2.7. Regardless of whether or not you keep that installation, you can ensure that python directs to the "Homebrew-ed" version by making sure that /usr/local/bin occurs before /Library/Frameworks/... in your PATH. 

In other words, remove the statement:

PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" 
export PATH


from your .bash_profile, or change the first line to:

PATH="${PATH}:/Library/Frameworks/Python.framework/Versions/2.7/bin" export PATH


This second version is somewhat useless, as there are two versions of Python that will be encountered before the Frameworks version (the Homebrew one in /usr/local/bin and the system version in /usr/bin). If you're curious where all of your Python versions live, you can check with which -a python, which lists all binaries named python in your PATH.