I ended up figuring this out. What I ended up doing is use the Eclipse export tool to export an ant build script for the three Java library projects. I then created a file called build-custom.xml which contains additional targets for copying the jars.
Next, I used the android update lib-project command on the Android library project to generate the build.xml for that project (as specified in http://developer.android.com/tools/projects/projects-cmdline.html). In order to include the Java library projects in the build, you have to copy them to the libs folder in the Android project. So I created a build file called custom_rules.xml in the Android library project that copys the jars into the lib folder. IMPORTANT: Also write a rule that removes the jars when done otherwise you will get Davlik Error 1 when you try and run in Eclipse.
You may or may not have an Android library project but the steps are pretty much the same for the main project as the library project. Just use the android update project command and then create a custom_rules.xml to copy the appropriate jars.
Edit:
After I used Eclipse to generate the build scripts for the basic Java library projects, I created a common.xml ant build file. This file basically looks like this:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project name="common">
<target name="clean">
<delete dir="build/libs" />
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary1" target="clean" />
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary1" target="cleanup-jars" />
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary2" target="clean" />
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary2" target="cleanup-jars" />
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary3" target="clean" />
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary3" target="cleanup-jars" />
<ant antfile="build.xml" dir="./AndroidSubProject" target="clean" />
</target>
<target name="samplesublibrary1">
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary1" target="all" />
</target>
<target name="samplesublibrary2">
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary2" target="all" />
</target>
<target name="samplesublibrary3" depends="samplesublibrary2">
<ant antfile="build.xml" dir="./SubJavaLibrary/SampleSubLibrary3" target="all" />
</target>
<target name="android-sub-project-copy-jars" depends="samplesublibrary1, samplesublibrary2, samplesublibrary3">
<ant antfile="build.xml" dir="./AndroidSubProject" target="android-project-copy-jars" />
</target>
<target name="android-sub-project-debug" depends="android-project-copy-jars">
<ant antfile="build.xml" dir="./AndroidSubProject" target="debug" />
</target>
<target name="android-sub-project-release" depends="android-project-copy-jars">
<ant antfile="build.xml" dir="./AndroidSubProject" target="release" />
</target>
<target name="android-sub-project-remove-jars">
<ant antfile="build.xml" dir="./AndroidSubProject" target="android-project-remove-jars" />
</target>
</project>
Then in the Android-Sub-Project, I added a custom_rules.xml file that contained the following:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?eclipse.ant.import?>
<project default="android-project-copy-jars" name="Copy required jars to lib folder">
<target name="android-project-copy-jars">
<copy file="../../build/libs/SampleSubLibrary1.jar" todir="libs"/>
<copy file="../../build/libs/SampleSubLibrary2.jar" todir="libs"/>
<copy file="../../build/libs/SampleSubLibrary3.jar" todir="libs"/>
</target>
<target name="android-project-remove-jars">
<delete file="./libs/SampleSubLibrary1.jar" />
<delete file="./libs/SampleSubLibrary2.jar" />
<delete file="./libs/SampleSubLibrary3.jar" />
</target>
</project>
I then created a main build.xml in the project root that includes and runs all the other sub build.xml files:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project basedir="." default="all">
<target name="debug" depends="clean, main-debug, android-project-remove-jars" />
<target name="release" depends="clean, main-release, android-project-remove-jars" />
<import file="common.xml" />
<target name="clean" depends="common.clean">
<ant antfile="build.xml" dir="./Main" target="clean" />
</target>
<target name="main-debug" depends="android-sub-project-debug">
<ant antfile="build.xml" dir="./Main" target="debug" />
<copy file="./Main/bin/main-debug.apk" todir="./build/bin" />
</target>
<target name="main-release" depends="android-sub-project-release">
<ant antfile="build.xml" dir="./Main" target="release" />
<copy file="./Main/bin/main-release-unsigned.apk" todir="./build/bin" />
</target>
</project>
Hope this helps!