I'm using the microtype package (microtype beta 2.5 build 08) to modify my document and I'd like to retain its functionality across all font shapes with the exception of small-caps (\scshape). How do I do this?
I'm asking this because microtype is not preserving the (\scshape) of section names listed in my table of contents whenever I use otf fonts (adobe caslon pro, adobe garamond pro, etc) that are loaded via fontspec. Instead, it's changing them to regular text. Whenever I don't load micro type, the text reverts to scshape. I'd like to keep the (\scshape) of the section names intact while using microtype without having to abandon use of the aforementioned otf fonts.
Here is what my toc looks like when microtype is enabled:

Here it is with microtype disabled:

I'm building my documents with Lualatex to facilitate loading of otf fonts and their usage with microtype. I notice this issue doesn't occur when using normal latex fonts.
Here is my code:
\documentclass[dotinlabels,nohyper]{tufte-book}
\usepackage{amsthm}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{fontspec}
\setmainfont[Ligatures=TeX]{Minion Pro}
\usepackage{fancyhdr}
\pagestyle{fancy}
\usepackage[unicode=true,
bookmarks=true,bookmarksnumbered=true,bookmarksopen=false,
breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=true]
{hyperref}
\usepackage{titletoc}
\usepackage{titlesec}
\usepackage{tocloft}
% If you do not load micro type below, small caps are preserved.
\usepackage[activate={true,nocompatibility},final,tracking=true,factor=1100,stretch=10,shrink=0]{microtype}
\hypersetup{linktocpage=true}
\setcounter{secnumdepth}{1}
\setcounter{tocdepth}{2}
%formatting for toc entries
\renewcommand{\cftsecfont}{\large\scshape\MakeLowercase}
\renewcommand{\cfttoctitlefont}{\scshape\MakeUppercase}
\renewcommand{\cftsecdotsep}{\cftdotsep}
\renewcommand{\cftsecpagefont}{\scshape}
%
\titleformat{\section}{\titlerule\vspace{.8ex}%
\Large\bfseries}{\Large\thesection.}{.5em}{}
\renewcommand{\sectionmark}[1]{%
\markboth{}{\thesection.\ #1}}
\newcommand{\hsp}{\hspace{20pt}}
%Chapter title Formatting
\definecolor{gray75}{gray}{0.75}
\titlespacing{\chapter}{0pt}{*0}{*5}
\titleformat{\chapter}[hang]{\Huge\bfseries}{\thechapter\hsp\textcolor{gray75}{|}\hsp}{0pt}{\huge\bfseries}
%
\begin{document}
\fancyhf{} % clear all header/footer fields
\fancyhead[RO]{\scshape\normalsize\MakeLowercase{\rightmark}}
\fancyfoot[R]{\thepage}
\tableofcontents{}
\chapter{Preliminaries}
\section{Mathematical Induction}
text goes here...
\newpage{}
test
\newpage{}
test
\end{document}
Renderer=Basic:\setmainfont[Ligatures=TeX,Renderer=Basic]{Minion Pro}. – Robert Jan 06 '13 at 18:38