This is very doable. Simply follow these instructions:
- Clone the plugin folder and rename to 'WP-Cycle2'
- Open wp-cycle2/wp-cycle.php
- Replace all 'wp_cycle' with 'wp_cycle2'
- Replace all 'wp-cycle' with 'wp-cycle2'
- Activate the plugin
- You will now see the cloned plugin in the Media admin menu
- Upload photos to WP-Cycle2
- Use shortcode [wp-cycle2] to post/page
I've cloned 8 WP-Cycle's for one website! You can also neaten this by renaming menu items etc.
Hope this helps.