Emacs copy a paste line with comment adds extra space / line
I guess you problem arises to an extend from continuing lines which get copied with the physical line break on screen. One way to avoid this and get proper mouse highlighting in Emacs, is running it as a separate GUI app. I installed GNU Emacs for Mac OSX and it runs perfectly with mouse selection capabilities: You can select with the mouse and continuing lines get copied as single lines as you want it.

GNU Emacs for Mac OSX  will pick up your normal .emacs configuration and if you do not like the GUI elements like the toolbar you can hide them on startup in the variable default-frame-alist.