Here's the sloppy way I attempt to save some time when in the same situation. This answer does not attempt to provide a resolution to the autobundle problems.

When you setup your cpan module on your 'base' system set it up with a huge cache (I set mine at 200 megs), also on the cache cleaning set it to 'never' I then setup my base perl on the clone system and just move the .cpan directory over. Install cpan.pm and let cpan.pm resovle the dependencies.

This is a serious cludge fix but it does save me time on a regular basis. There is a significant time saving in not having to dl all the bundles. I should also point out that more than half the time the bundles I have in the cache have been updated so there is still dl time involved.