If you have any problem using the "RunAnt" commandline to build (using Ant "headless" Studio to do the J2EE taks like ejbDeploy and EarExport) please let me know. It works. You just need to edit the "RunAnt.bat" to set your workspace.
5.0) in WSAD-v5.0x you cd into wstools\eclipse\plugins\com.ibm.etools.j2ee.ant_5. 0.x
5.1) in WSAD-v5.1x you cd into wstools\eclipse\plugins\com.ibm.etools.j2ee.ant_5. 1.x