I went with a 309 ci "Y" in mine.  (292 bored .30 over and 312 crank)  I replaced the stock 3 speed with a 3.03 Toploader full syncro transmission with minor modifications (truck trans not car).  That allowed me to keep the column shift, handle the extra ponies and have syncros in first.  A BBF is cool too.  If the price is right that may be a fun way to go as well.  As said here by others it depends on your goals and budget.  I have two 56 F100's and like Bing will be happy to help with any questions or suggestions.

   

1956 F100 Big Window 309ci Y-block,  1956 F100 small window 272ci Y-block

Greg.  Mountains of North Eastern CA

Also,  If the 9" rear end is out of a '57-'64 Ford pickup it will bolt right in and be the same width if using the smaller rear drum brakes off the original rear end.  The drive shaft will need to be modified of course.  I also advise better brakes if your planning on making more hp and therefore going faster.  Again this depends on your goals and budget.

   

1956 F100 Big Window 309ci Y-block,  1956 F100 small window 272ci Y-block

Greg.  Mountains of North Eastern CA