Dean,
The core problem here is that you might be assuming too much of a connection between Ant and Eclipse when it is run from the IDE, so let me clarify: when you fire up an Ant script in Eclipse, it is launched in an external instance of Java, so it is no different than launching it from the command line… so forget about any continuity between how your Eclipse project is setup and how the Ant script runs.
If you get into the habit of writing your Ant scripts to run from the command line, then that will take care of the issue. In the case of building this app, I’m not surprised that these JARs are required, just point to the jsp-api.jar and servlet-api.jar files from your Tomcat install that you are deploying to, that will take of the problem.
Don’t point to the Tomcat install that you found under Eclipse’s plugin dir, this version is a trimmed down Tomcat that is used exclusively for hosting the help files, it is not what is actually run when you use MyEclipse (unless, I guess, you configured it that way). What we intended you to do is go download Tomcat from Jakarta’s site and install it someplace else (c:\Java\tomcat5.0 for example) and then setup the connector to launch that instance. So in your ant script point at the 2 files I mentioned in c:\Java\Tomcat5.0\common\lib and include them in your <classpath>, so your targets compile.