There's plenty room for a five speed or auto in that body. In 58 the big cast iron Borg-Warner M-8 auto was available. A three speed with add-on overdrive was also used and was pretty long. The trans tunnel isn't very deep as the body sits so high... only protrudes 3-4" up into the floor.
ramzoom -- just make sure you put that upper brace back in! That's the main support for the front fenders. I see it cut out all the time, and sometimes left out. A bolt in mod will work, maybe make a tubular brace -- take a piece of steel 1" conduit and flatten each end in a vice, then drill and bolt to the stubs left from the brace. The engine originally went in (and came out!) from the bottom, that's why the brace is welded in. The fenders will get a bit loose without that brace, or something similar in its place. That Q4 sure does fit good! Do you have a stock intake? If you do, could you see if it would fit on the engine in the car? Sure would like a pic of that even if it doesn't fit!