Hello,
The internal organ IDs are different between volumes which allows you to retain settings for volume I separately from volume II, and thus treat them as two different instruments. Due to this you cannot easily transfer settings from volume I to volume II. There were also some modifications to the samples from volume I for this version which we are offering a patch for, therefore some of your settings may not transfer properly due to some sample changes (minor however). I will post a new topic shortly with details for this patch for the volume I samples and ODF.
You can find the volume I patch here:
http://www.milandigitalaudio.com/downloads.htm
ALso the same situation applies between the volume II original and extended versions, they each have their own IDs, thus any settings you create for the volume II original version will not transfer over to the extended version.
Regarding the lines above and below stop names. These are from the original organ. I am not aware of the history behind them, perhaps we can try to find out.