To configure Mozilla's compile-time options, type ./configure from the root directory of the Mozilla source tree. To get a full list of compile-time options, type ./configure --help. Some things to verify before doing a production compilation include verifying that environment preferences (mail vs. no mail, calendar, ldap, etc.) are set and making sure that the crypto package is enabled.
For simplicity's sake, I generally use a simple build script like the following to configure Mozilla.
#!/bin/sh MOZILLA_OFFICIAL=1 export MOZILLA_OFFICIAL BUILD_OFFICIAL=1 export BUILD_OFFICIAL ./configure --with-x --disable-calendar --enable-crypto --with-system-nspr --disable-debug --enable-extensions --enable-optimize --without-system-zlib --without-system-jpeg --without-system-png --without-system-mng
Once you have your patches applied, config files modified, and options set, simply build Mozilla with gmake by typing ./gmake in the root directory of your source tree, and then create your tarball by typing gmake in the xpinstall/packager directory. This will drop the tarball in the dist subdirectory just beneath the root directory of your Mozilla source tree. Just move that package to /usr/local, unpack it, run it once from the command-line as the user who built the package (the command is /usr/local/mozilla/mozilla), and you are nearly ready to browse.