This sounds reasonably easy.
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How is the press actuated? Is it just a 5v signal to go up, and a different 5v signal to go down?
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How did you want to set the retract and bottom heights? An LCD screen? A web page on your local LAN? Hard-coded into the program? Did you want a system that lets you "nudge" the position of the arm, and then you hit a "Set" button to set the top/bottom position of the stroke?
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Are we worried about acceleration and deceleration, or will a simple off/on do?
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What type of rotary encoder? Does it use i2c? A bunch of pins? Can you post a link to the data sheet?
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What controller buttons do you want? Just a single one that says "stamp"? If you press it while the stamp is in progress, then the stamp is cancelled?
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Do you want some sort of failsafe - if the arduino activates up/down and the encoder doesn't start changing, then cancel everything?
Assuming this is a nice slow press with a simple up/down which doesn't have any sort of speed control (the valve is either open or closed), I suggest an "up" and "down" button, a "set" button and a "stamp" button. Up and down move the press manually. Holding down "set" and pressing "up" or "down" sets the top/bottom position by reading the rotary encoder and saving the value. "Stamp" runs through a stamping cycle, any button press cancels the cycle.