congrats on getting your shoebox, i'm in the middle of putting a 49 coupe back together.
there isnt anyplace better for ford flathead info than the ford barn. i just finished putting my first flathead together with the help of this site, a few books, and my dad.
for questions specific to your car, register with
http://www.shoeboxford.com/ and checkout the discussion forum. lots of great info on 49 - 51 fords there.
and i'd recommend buying a green bible:
http://www.amazon.com/1949-1950-Serv.../dp/B0007IN9LW
the book covers everything from engine and transmission problems to installing a new windshield.
good luck, don't forget to post some pictures to!
john.