Does your FIL had any half siblings still living? It might be worth asking them (if still living) or nieces/nephews from any half siblings to take a test. That way you can compare results and work out the matches... the ones that don't match belonging to your FIL are the ones that will give you a clue to where to start looking for the paternal line.
I have recently discovered a great way to analyse these matches.
I am a bit late to the table with upgrading to RootsMagic 10 which has improved DNA logging, I have started combining this with one month trial of Ancestry pro tools which allows you to see your matches dna results, by entering that into RootsMagic, I have found some very useful clusters. and it has certainly revealed how most of my matches relate to one another.
I have found someone who was adopted with a name change and managed narrowed down his parentage to one of a set of brothers using his results against matches with my tree. I have also managed to work out quite a few of those private trees with the tree owner called John Doe or as one of them is called "Apple Payment card"
I found her through her match results to her mother which only showed up when using the pro-tools.
It does help to have already researched everyone back to at least 4th cousin level, so anyone you don't recognise in the matches is likely to be on your paternal FIL's side.
The only matches I have which don't make sense is a large swathe of people who tested in the US and they seem to want to trace their trees back to the Mayflower and I'm pretty certain my family were not early pioneers. I have also found one or two which I think Ancestry has made a blip and don't belong on my paternal side as they match with my maternal side... they seem very obvious errors which might throw someone looking for parentage off track.
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