EDIT (July 25, 2012)
There is a small bug concerning the column separating space in the version below. I fixed that and wrapped up the whole parcolumns patch in a tiny package named parcolsx, so that you can do something like:
\documentclass{book}
\usepackage{geometry}
\usepackage{parcolumns}
\usepackage{parcolsx}
\usepackage{lipsum}
\begin{document}
\chapter{Chapter heading}
\begin{parcolumns}[%
sloppy = true,
sloppyspaces = true,
nofirstindent = true,
colwidths = {1=0.43\textwidth, 2=0.53\textwidth}
]{2}
\colchunk[1]{\small\indent%
\lipsum[14]
\lipsum[15]
\lipsum[16]
\lipsum[17]
}
\colchunk[2]{\Large\indent%
\lipsum[10]
\lipsum[11]
\lipsum[12]
\lipsum[13]
}
\end{parcolumns}
\end{document}
Note the additional key/value pair alternate = true in the arguments of the parcolumns environment. This way the alternating columns can be activated at will.
The package parcolsx to be saved in a file named parcolsx.sty:
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{parcolsx}
\RequirePackage{changepage}
\strictpagecheck
% add the additional boolean key `alternate'
% to the `parcolumns' environment
\newif\ifpc@alternate
\define@key{parcolumns}{alternate}[true]{%
\pc@boolkey{pc@alternate}{#1}%
}
% slightly modify the `\pc@placeboxes' macro to distinguish between odd
% and even pages, if the option `alternate=true' was passed to the
% `parcolumns' environment
\def\pc@placeboxes{%
\global\let\@tempa\relax%
\hb@xt@\linewidth{%
\vfuzz30ex %
\vbadness\@M%
\splittopskip\z@skip%
% odd is the default
\ifpc@alternate \checkoddpage \else \oddpagetrue \fi%
\ifoddpage
% count up from 1 to N_col
\count@\z@%
\loop\ifnum\count@<\pc@columncount%
\advance\count@\@ne%
\pcx@placeboxes@body%
\ifnum\count@<\pc@columncount%
\strut\hfill\ifpc@rulebetween\vrule\hfill\fi%
\fi%
\repeat%
\else
% count down from N_col to 1
\count@\pc@columncount%
\loop\ifnum\count@>\z@%
\pcx@placeboxes@body%
\advance\count@\m@ne%
\ifnum\count@>\z@%
\strut\hfill\ifpc@rulebetween\vrule\hfill\fi%
\fi%
\repeat%
\fi
}%
\@tempa%
}
% the fraction of `\pc@placeboxes' that does not depend on the page
% parity
\def\pcx@placeboxes@body{%
\expandafter\ifvoid\csname pc@column@\number\count@\endcsname%
\hskip\csname pc@column@width@\number\count@\endcsname%
\else%
\expandafter\setbox\expandafter\@tempboxa%
\expandafter\vsplit\csname pc@column@\number\count@\endcsname%
to \dp\strutbox%
\expandafter\@tempdimb\csname pc@column@width@\number\count@\endcsname%
\hbox to \@tempdimb {\vbox{\unvbox\@tempboxa}\hfill}%
\fi%
\expandafter\ifvoid\csname pc@column@\number\count@\endcsname%
\else%
\global\let\@tempa\pc@placeboxes%
\fi%
}
On a side note: that patch also fixes the incompatibility of the parcolumns with the wrapfigure package. I will comment on this in the other thread: Wrapfigure-Minipage Woes
Original answer (including column separator bug)
You ask for many different things and your sample document contains a lot of stuff that might not be helpful here. However, I might have found a solution for your column switching problem.
Please see this more minimalistic example:
\documentclass{book}
\usepackage{geometry}
\usepackage{parcolumns}
\usepackage{changepage}
\strictpagecheck
\usepackage{lipsum}
\makeatletter
\def\pc@placeboxes{%
\global\let\@tempa\relax%
\hb@xt@\linewidth{%
\vfuzz30ex %
\vbadness\@M%
\splittopskip\z@skip%
\checkoddpage\ifoddpage
\count@\z@%
\loop\ifnum\count@<\pc@columncount%
\advance\count@\@ne%
\my@placeboxes@body%
\repeat%
\else
\count@\pc@columncount%
\loop\ifnum\count@>\z@%
\my@placeboxes@body%
\advance\count@\m@ne%
\repeat%
\fi
}%
\@tempa%
}
\def\my@placeboxes@body{%
\expandafter\ifvoid\csname pc@column@\number\count@\endcsname%
\hskip\csname pc@column@width@\number\count@\endcsname%
\else%
\expandafter\setbox\expandafter\@tempboxa%
\expandafter\vsplit\csname pc@column@\number\count@\endcsname%
to \dp\strutbox%
\vbox{\unvbox\@tempboxa}%
\fi%
\expandafter\ifvoid\csname pc@column@\number\count@\endcsname%
\else%
\global\let\@tempa\pc@placeboxes%
\fi%
\ifnum\count@>\z@%
\strut%
\hfill%
\ifpc@rulebetween%
\vrule%
\hfill%
\fi%
\fi%
}
\makeatother
\begin{document}
\chapter{Chapter heading}
\begin{parcolumns}[%
sloppy = true,
sloppyspaces = true,
nofirstindent = true,
colwidths = {1=0.43\textwidth, 2=0.53\textwidth}
]{2}
\colchunk[1]{\small\indent%
\lipsum[14]
\lipsum[15]
\lipsum[16]
\lipsum[17]
}
\colchunk[2]{\Large\indent%
\lipsum[10]
\lipsum[11]
\lipsum[12]
\lipsum[13]
}
\end{parcolumns}
\end{document}
I slightly modified the macro \pc@placeboxes from the parcolumns package, so that it distinguishes between odd and even pages. The actual check is done using macros from the changepage package, which is why it is loaded in the preamble. You will have to compile at least twice, since this relies on page lables.
The resulting output is, I think, what you desire, i.e. the columns interchange at every page break:
I have not bothered about the margin notes and you might experience side effects. If that is the case you should better open a new question and tackle one problem at a time.
EDIT (July 22, 2012)
The parcolumns package works in two steps: first, the contents of each
column is typeset in a box. This is done by the \colchunk command.
Second, for every line on the output page one line from each column box
is extracted and placed on the page. That is done by the
\pc@placeboxes macro.
So, assuming N columns, the original \pc@placeboxes in principle
does the following: For colums i=1 up to i=N the first line of the
i-th column box is cut and pasted on the page. If i<N a column
separating space is inserted.
I simply hooked into this macro and inverted the order on every second
page: the modified \pc@placeboxes does exactly the same as the
original one for odd pages. However, for even pages it loops from i=N
down to i=1 when cutting and pasting the lines from the column boxes.
The problem with the wrapfig stuff very likely stems from this
two-step approach. Having not looked into the wrapfig package I can
just guess that it uses \parshape to modify the shape of the typeset
paragraph. This will influence what is typeset into the column boxes.
Apparently, things go wrong when the lines of the column boxes are
distributed on the page. I can not, unfortunately, offer a solution for
this issue at the moment (actually I hoped that some of the TeX gurus
here would have a suggestion for you).
Best Answer
I would use the parcolumns package, personally. You can use the colwidths option to set the widths of each column to whatever you want. See its documentation.
Creating larger than normal margins and using \marginpar might also be a possibility. (Perhaps with the marginnote package.)