If you want a simple solution to solve the clearance issues and get the engine running ( may well do without altering anything) I'll stick with my earlier suggestion of filling the voids. Next option up the list would be a new piston about 18mm long which will compensate for teh under size piston and shorter crank throw at one sitting. Lastly if you do go for remaking the crankshaft it looks very slender in those images so think about increasing at least the main shaft, pins can stay the same.
Looking at the drawings there is plenty of thickness in the end covers to drill and tap a couple of small holes say M2 to M3 so that a suitably drilled and CSK infill can be added, for the top cover the plug can be JBWelded into place to fill the excess piston rod nut recess. Make the infills 38mm diameter so air/steam can flow all round and get to the face of the piston.
Talking of air getting to the piston make sure you notch between the cylinder wall and steam passage as per drawing, as it is now the cover will fit tight against the end of the passage.
Looking at a couple of videos of the original JLS engine if notched up it looks to run at a fairly modest speed maybe 50-60rpm so you can see the bits moving and it's not all a blur so there is hope yet.