My father in law is buying a 9' 6" fiberglass boat and he wants to power it with an electric trolling motor. How many # thrust do you think it'll take?

I would think a 35lb thrust should be sufficient

The minn-kota site recomended the 30# for boats up to 14' but we have a canoe for duck hunting that that has the 36# and it even seems slow. Not sure what kind of speed he wants but its easier to make a powerful motor go slow than the other way around.

http://www.minnkotamotors.com/_docs/motor_specs.pdf

http://www.cabelas.com/cabelas/en/templates/links/link.jsp?id=0011592014194a&type=product&cmCat=Search_Results_NYR&returnString=No=80&Ne=2510&Ntt=trolling+motors&noImage=0&QueryText=trolling+motors&Ntk=Products&_requestid=11536&Ntx=matchall&N=3238&cmcat=search_redir&returnPage=search-results2.jsp

Will that do it?

That 40 lbs should be fine. A trolling motor is just that. It is used for trolling not high speeds to travel from spot to spot.
I had a 35 Minkota on my 12 ft aluminum and that went well and would last all day. I used it on some pretty decent sized lakes also. Not sure how heavy the fiberglass boat is though.