FIrst of all, if you have imported the Gedcom twice, go back tot he backup you were prompted to make before you imported the Gedcom.
Now the New file that you put the data into is a very good idea. It is what I always do, when I get a Gedcom file. Run Match/Merge in that and then export that into a new Gedcom file to put into your data.
If it is from some one you plan on sharing a lot of information with, and you are both using PAF 5, one of you should get all the data of both of you then afte you have combined it send back what bleongs to them as a Gedcom. This means in future M/M will be easy usy the URIN.