You're not making any sense, what do you mean by 40mm jug? The difference between a jug used for the 40mm stroke and the 38mm stroke is only around 1mm in height, as was mentioned above there are short and long rods in both strokes and high and low holed pistons and you can't just mix and match all willy nilly from one to another.
Generally short rods use low holed pistons and long use the high, not all ways but most commonly. If you put a low holed piston on a long rod or a short rod intended for high holed piston it will protrude above the deck and there is the 3mm, using rtv as gaskets once it cures shrinks to less then the normal gasket thickness and again posses more cylinder drop and clearance issues as heat cycles will reduce it again as re torque is required.
Bent crank ? How would a bent crank make the piston protrude, if the crank was bent it would not rotate smoothly but can not alter the stroke out ward if any thing it would reduce it and may cause piston to drag on a portion of the cylinder wall adding to the resistance in rotation of the crank.