Hi Craig,
The method for selecting an Alternate Item number within Add/Modify/Delete Items in Inventory does not describe how the data is actually stored in the item file. IC can only bring up an item finder, and whichever item you select, the 'Alternate Item Set number' from that item is also applied to the item you are editing. It might be more confusing if in IC Edit Items you only could see the Set Numbers...
If you print the Alternate Item report within IC, you will see what is happening more clearly if 3 or more items all belong to the same set. This is about as close as you will be able to come with any version of a report writer, be it Quik Reports DOS or Crystal Reports for Adagio. This would involve creating a group by the Alternate Item Set - but this might incorrectly affect your intended report.
This is the way IC was configured all the way back to version 5.1 at least, and when I looked at the tables for QR DOS for all versions back to 5.1, they all say 'Alternate Item Set'. Your version of Quik Reports DOS will not affect what you see; what is important is the table you are using.
To answer your question, there is no way to link to a 'real' item number because this is not how the data is stored.