I would use Photostream to get all of the photo's off of your devices and onto your Mac as it will take care of the duplicate issues you are having.
The iPhone is already taken care of, as all of the camera roll photo's should be in your Photostream already. As for the iPad and your iPhoto modifications, you can use the iPhoto "Edited" album that the app has. This album contains every photo that you have modified in iPhoto. Open the iPad's iPhoto "Edited" album, turn on the thumbnail grid, select and hold a photo to enable multi-photo-select and then select all of the modified photos.
Once you have selected all of the modified photo's, use the Share button to send them to your iPad's camera roll. Photostream will then sync those photo's to your Mac's Photostream. No duplicate photo's.
Also, in the future, if you take pictures with your iPhone and they arrive in your iPad's Photostream, you can save them to your iPad Camera Roll and they do not get re-synced as a duplicate to Photostream. This lets you save local copies to each device's Camera Roll if you want and you don't have to worry about syncing duplicate's from Photostream to your Mac.
Hope this helps!