a couple things that you might wanna think about, adding the hand wheels on the back end of the motors is a neat idea, i thought about this myself, till someone pointed out that the handels aren't ballanced, and will add vibration to the system when in cnc mode.
something else to think about, by keeping the z axis hand wheel, again ballance, and you will be adding more load to the z axis system, meaning that it will take more torque to turn the screw. I would also think that this would add a considerable noise component as the gears for the z axis arent exactly what i would call perfection.
Michael over at cnc fusion is a really great guy and really helped me out when i did my conversion. we emailed back and forth i dont know how many times, untill i fully understood what i was dealing with. The fact that he's basically my neighbor didnt hurt his running in the decision on what product to go with as well(hes just a couple hours down the road from me)
extending the quill down for milling operations is not something i would suggest, it adds more lever action to the whole machine and could introduce additional flex and possibly more chatter when machining. Mine is in the upright and locked position and thats where it stays.
feeding back to software from the motors would need to be handeled by an encoder, or some kind of DRO unit. I suppose if you really wanted to get off into it, you could work up the electronics to try and feed back the motor pulses, but the problem is going to be when you land between steps, or just hit a step but then rock back to the previous detent, this will introduce errors... not to mention that as speed changes, voltage out will change, and this could effect the sensing.
not to mention that depending on the drivers your using, feeding back when thier not on could cause the drivers to fail.
really the only way to do it reliably is with encoders or a dro. go and get yourself the mach 3 instruction book, it talks about doing just that....
http://www.machsupport.com/docs/Mach...all_Config.pdf start on page 52 of the pdf, section 4.10 linear encoders.
half stepping a 200s/r motor, with a 10tpi screw gives .00025 inches per step,
2*200*10=4000steps/inch
your main issue os going to be resonance in the motor. half stepping has issues at certain rpm's of the motor/screw/coupler system. resonance is a bad thing when talking about stepper motors, and should be reduced and or avoided if at all possible. it can cause lost steps, which translates to messed up parts, and or possably worse, much worse depending on how bad it is. (can you say crashing the endmill into the table?)
the other problem is gonna come in when you convert over to the 5tpi screws, it'll drop your resolution to .0005 per step. if this is an acceptable resolution, then ok, but if your doing some machining, say, a long low angle part, where the angle isnt parallel to an axis, say 5 or 10 deg off, then you may notice some resolution stepping. this probably wont be a major factor as we're only talking about a half a thou, but if you get into ultra precision stuff, or if theres some backlash in that axis' travel, it may become very evedent. on my system i'm running 200step/rev motors, 10 microstepping drive, 5tpi ball screws(cncfusion) and my theoretical resolution is .0001 and i'm more than happy, and i can still get rapids over 100ipm.
as for drivers, i'm running gecko 203v's, and i couldnt be happier. I love the "vampire" drives, cause you, and i'm quoting gecko here, you cant kill 'em. all sorts of safeguards, short protection, and stuff like that. if your not super on your game, you can blow up some of the other drivers out there, and all you did was sneeze hard. I gotta say, gecko makes a good product, and the 203v is my personal favorite. Keep an eye on the gecko site, they sometimes put thier stuff on sale(i happend to catch them on sale when i got mine)
something else, if your not already familiar with the terms resolution and repeatability, learn what they mean and the differences between them. i know that this was a hurdle when i first started into all this, and knowing the difference has helped me to become a better cnc operator.