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You are correct that it is just a matter of which port is intake and which port is exhaust. That is why if you are looking for a York the best one is the 210 model and it will either be a 210L or a 210R, the L and R is what designates the intake port.
When mounting the York in the upright position it doesn't matter which one you get BUT if you mount it on its side then you have to make sure you get the proper York (intake side must be the top fitting).
If it matters at all I recently got a long stroke york from an older volvo, turned colckwise , and looking at it from the clutch side, the intake is on the right.