The Reference and Users' guides are currently set up to be built with special Sandia-specific class files that you won't have access to. These class files make the documents look exactly the way Sandia wants all external publications to look.
However, if you look at the top of Xyce/doc/Reference_Guide/Xyce_RG.tex, you'll see this text:
% When compiling at Sandia, uncomment 'sand' and SANDreport
% Outside of Sandia, uncomment 'report' and scrreprt:
\documentclass[11pt,report]{SANDreport}
\usepackage[sand]{optional}
%\documentclass[11pt,letterpaper]{scrreprt}
%\usepackage[report]{optional}
Change this to:
% When compiling at Sandia, uncomment 'sand' and SANDreport
% Outside of Sandia, uncomment 'report' and scrreprt:
%\documentclass[11pt,report]{SANDreport}
%\usepackage[sand]{optional}
\documentclass[11pt,letterpaper]{scrreprt}
\usepackage[report]{optional}
and "make" in the Xyce/doc/Reference_Guide directory will produce Xyce_RG.pdf.
A similar modification of Xyce_UG.tex in the Users_Guide directory will get that file ready for "make" to create Xyce_UG.pdf.
You will have to modify Xyce/doc/Reference_Guide/Makefile and Xyce/doc/Users_Guide/Makefile to make it create any other formats. We have never done so, and so cannot help you there.