The Hydrive engine has an extra hole in the rear casting which is the return line for the Hydrive. It can be plugged inside the oil pan 1/4 " pipe plug, if memory serves me.  The oil supply for the Hydrive comes out of the back of the oil gallery  and it needs to be plugged just as found  on the 1950 engine. 

As long as the crankshaft has 8 bolt holes your 50's flywheel will fit even if it is a 4 holer.  I have heard, but never seen that some Hydrives had 6 holes in the crankshaft flange. If that is the case, it might be difficult to fit a flywheel.  Any that I have ever seen had 8 holes.   

A pilot bushing may need to be inserted into the shaft as well.

As  for the oil pump, it has a pressure bypass built into the cover and it can be left in place, however, it would be better to substitute a regular pump and check that the usual bypass on the left side of the block has the regular (unpainted) spring inside it. (same as the 50)

Apart from that, the engine is a bolt for bolt swap into a 50.

I believe the rear main seal on the High drive engine is different as it was the supply path for the oil to the transmission (hydrive shared apx 11 quarts of engine oil with the engine) Not an expert on the HY drive by any means, but this has come up a couple of times, usually by people changing rear mains.  Apparently one application has a hole bored through it where one would ask Wonder what that is for?????

This is a hypothetical question, but I am interested in the answer. Recently I could have obtained a '53 Hy-Drive engine in order to do a "minor" rebuild for the experience. I would have done the bearings, rings, valves, etc., anything short of expensive machine shop work. If the engine was good enough, I thought it could also be kept as a spare for my '50. How different is the Hy-Drive engine from one made to work with the manual transmission? All I know so far is that the carb. and the oil pump are different, and probably the flywheel and bellhousing.