Bob,
Welcome to the site and welcome to y blocks. All Y blocks have the same side bosses for motor mount hookups. The difference you will find up front would be the truck/Thunderbird timing cover is different from the passenger car timing cover because this is where your front hard mount hooks up. (depending on what 239 is in your car, you may have the timing cover that takes a smaller water pump - this would be the EBU block. I "think" the EBV takes the 5/8" shaft water pump) You may already know that the truck bellhousings are different because they have ears underneath that are used for side mounts and on the trucks the engine blocks side mounts are not used. In your case, you are reusing your own bell, so no problems there. ALL Ford Y blocks from the 239 to the 312 will work on your bellhousing with 0 issues.
The difference you will find with engine cores to rebuild (or purchasing a used, running engine) is that the Truck/Thundebird accessories are different from the passenger car accessories (there are some nuances that are solely particular to Tbird as well). However, all of those things can be switched from block to block, and there are items on your current 239 that can be switched to another block quite easily.
You mentioned water pumps and fan/spacer depth. The 239 did have a smaller water pump from the other Y blocks, and there were later Y blocks that had larger diameter shafts (3/4") on them. Watch for that. I believe your water pump should have the 5/8" shaft. Your current spacer, pulley, and fan should be "swappable" from engine to engine, but you will have to purchase a water pump.
There are plenty of fellas on this site that are much more knowledgeable than I am. Once they get the chance I am sure they will give you more details and correct any misinformation I may have but I do believe I am spot on here.
Daniel JessupLancaster, California
aka "The Hot Rod Reverend" 
check out the 1955 Ford Fairlane build at www.hotrodreverend.com