It could be the encoder but I am thinking the Z drive or upstream of it. You overdrew current which is felt by the motor/drive evidenced by it getting hot. The motor survived but the drive took the brunt of the over current. Can you stick one of the other drives in the Z position? You have essentially done that when you piggy backed the Y drive to Z motor but that does not eliminate what's up-stream of the Z drive just yet. As you say it's not a Break Out board per say but whatever it is, it gives the Gecko its move instructions. The encoder is essentially feedback so it might be the problem but intuitively the drive or its control seems more likely to have failed. How tough is to get a spare encoder? Any existing parts servcie on this machine? Pictures are always good. You almost got this.


Like this one: http://cnccookbook.com/CCMillCNCConversionHome.html

I did take working Gecko drive from Y, and put it on the Z. Z still didn't work. I also took Z drive and verified it worked on the Y. If that maks sense... drive is working correctly.

As you can see in first pic, my Z drive is close to where parallel wires come into cabinet. They seem to go directly to drive.

Where does your parallel port connect to? is it just bare wires taken to each drive/component or is there a plug on the end that goes to a board and then wires from that?
Hood

thats what i was hoping you could tell me from bigger pic. it seems like they go direcly to drive

Can you not see the cable that comes from the computer? Trace it to the cabinenet and see if it goes to a board or if its just wires that come out the end of it that go to the drives etc.

In the pic I cant really tell where the cables go, they seem to go to a breakout board  (BOB) of sorts, I think its the green and yellow wires? If it is then you could swap the Z for another axis on that BOB and see if the problem follows the wring change or stays with the axis,

Hood

On the zoomed in picture the blue terminal strip to the right with all the yellow & green wires are hooked to step and direction on each drive. If you look closely it looks like where the computer ties in from the port. You see a dark connector betwen the terminal strips below.  Compare signals coming from Z(terms 6 &7) and Y (4,5) ect. I bet something is corrupt off that so called break out.

I am a bit puzzled what the 2 boards in the middle do, 1 has a bunch of black capacitors (left) and the other looks like some sort of logic card(right, green board blue relays and chips). Maybe these are amplifiers...to handle feed back?? They tie together. Keep going!

Think the middle cards may well be spindle control boards.

Hood

Here's a better picture.

Hood id correct the middle ones a re spindle control.

The thing is, the Gecko faults...WITH NO MOVEMENT AT ALL ABOVE ABOUT 30% ON LIMIT. Doesn't that rule out the bob pins?

The encoder is constantly giving feedback to servo at all times, correct?

I'm almost sure the reason Z isn't moving up and down is because I can't turn limit up enough (without a stationary fault) on Gecko drive so it has enough voltage to move servo.

Never used Geckos or DC servos so cant really help on them, only used AC servos.
What is the black wire hanging loose?
BTW thatBOB is just a basic connection board by the looks of it so unlikely there is a problem with it.
Hood

Those are encoder wires. Had them off testing them.