Fascinating project. What aspects of the equipment are you controlling?
Firmata is a good place to start, but I've noticed some lag, I haven't used it in years though.
I would argue that if you are not writing your own firmware, Arduino is overkill for this application. If what you need is Pd to sequence the movement of two steppers, than there are a host of existing options which do not require an Arduino. Googling "USB Stepper Controller" gives you several options, some even targeted at novice/hobbyist uses.
If you do decide to use Arduino, the experience of figuring out the language enough to do what you need will certainly benifit you in the future. ESPECIALLY if digital control of analog equipment is the kind of thing you are in to!