Hi,
Which PICKit3 version do I need? PG164130 or DV164131
What you NEED is the PG164130, that is the actual programmer/debugger itself. The DV164131 also includes a little development board which may or may not be useful.

100 iterations per minute, each 2*4 inches long (max) is 800 inches per minute average velocity, the peak velocity will need to be much higher since you need account for acceleration/decceleration - This might not be THAT easy.... Using a pinion with a 2" effective circumference means the motor must turn 400rpm to reach 800ipm (again faster than that in reallity) but there's only two revolutions of travel so the acceleration must be sort of insane.... Using a smaller pinion means the motor needs to trun even faster (bad), reduces torque requirement (good), have less load carrying capabillity (bad, but can be adressed by using a wider pinion) but at one point you still need to fit to a shaft so it can't be made THAT small.
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I have a feeling this requires some pretty serious motor/drive combination, a stepmotor may not be the best. I'd probably look at a ballscrew driven linear stage with a high pitch screw, something like 10-20mm (or 1/2" - 1") driven by a servomotor. Plenty available on EBAY.

/Henrik.

BTW, using encoders on stepmotors is very uncommon as it kind of defeats the simplicity of an open loop stepmotor. There ARE closed loop systems available but then the motor/drive behaves more like a servosystem than a stepmotor system. You read on DIY CNC lists and forums that step motors are notorious for loosing steps but that only happends when you're operating them outside of their limits - ie you're asking more from the motor than it can deliver. Properly dimensioned and used it is as reliable and rugged as a servo system but each have their benefits and drawbacks.

Geckodrive used to be great, my G210's are 14 years old and still going. However, if I'm not misinformed the founder has cashed in and left the building and it's not what it used to be - or so I hear. Still great step motor drives though!