If the unit listed on ebay at
http://www.ebay.com/itm/IH-Farmall-...40-130-Super-A-100-Super-C-/221605120016?hash=item3398b1c810:g:So8AAOSwcldUZYLW (I tried to find a photo in my files but no luck) is what you are trying to remove, it is possible that one of the bolts that hold the unit to the main case was stripped at some point in time and a replacement was dropped through and inserted from the top of the housing, or the head was snapped off at some earlier time. Otherwise, all the bolts should be threaded into the main housing.
I presume you have drained the fluid so you do not get a lap full when the housing comes off.
What I would do is make sure the nut is off the bolt that is sticking out the wrong way, then pull the housing. Once it is removed you will have easy access to the remaining bolt, or if it is a previously broken bolt it can then be drilled and an easy out used to remove the stub.