Are you saying that each column in the first table has its own unique paragraph tag applied to the text in each row in that column, and that what you want as an output is a generated list that pulls the text tagged with paragraph tags used only in certain columns but keeps all the items in the same row together?
If so, bog-standard FrameMaker can't do what you are describing. If it were one or two tables, I'd say just copy and paste the rows into a new table, delete the unwanted columns, and sort, but if I understand you correctly, you've got far too many documents and tables for that to be anything but tedious and very, very time consuming.
I suspect that a script is what you will need, and unfortunately for you (and me), I have yet to learn how to script. There are some script writers on this forum, but you'll need to post your question in the FrameMaker Scripting forum to get real help. I'm not a mod, or I'd move it for you. 
Russ Ward may be able to help you write the script, and there are also a number of people who write scripts for a fee. Personally, I've worked with Rick Quatro of Carmen Publishing and have been very happy with both the custom script he created for me and his standard products.
(Mind you, if you're only planning to do this once, BFME can work and actually be faster than the elegant solution of a script, but if this is going to be a regular task, invest in a script.)