The easest way i can explain unipolar vs biploar is like this. Imagine you have a coil, like one in a motor, and lets call the connections to it a and b. you can apply power to it with a + and b -, or with a - and b +. in unipolar you pick one or the other and use it exclusivly. in bipolar, you use both all the time. thats the super simple version...
chances are that you can find motors that you will be able to use for both, and if you do mis wire something, i would think that it would be more likely to kill the drive than the motor.
if you can figure a quick release system for the handles, then i really dont see a problem with it, there are some that might "give you the business" about it, but its your machine, and if thats what works for you, then i say go for it. In my mind i picture somethng like a race car steering wheel release mech.
my experience with encoders is fairly limited, but what i do know is that they do need to mount somewhere on the shaft, i have seen far end encoders, and motor mounted ones. if you mount it on the motor, then i would think that it would go onthe back end shaft. If it were me, and i were considering getting and using encoders, i would just get the motors with them already installed, just to simplify my life. The other option would be to get the encoders, and mount them on the far end of the screw, but this has its advantages and disadvantages. Encoder pricing will depend largely on how many divisions it has, or how accurate its supposed to be.
one thing that you might consider is using a jogging pendant. I just recently saw one online for about $90 that was usb interface, and would allow you to jog each axis down to the single step.. I'm seriously considering getting one of these for my machine, as i sometimes would like the ability to operate in a "manual mode"
i wouldnt think that it would be very expensive to set up a touch off tool height system, i havent tried it yet, but i think its a great idea. Perhaps someone else can give us some input on this.
I dont see a major problem driving the z screw from the top, and if you wanted to get creative, i bet you could still set it up with some mechanical advantage...
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