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Funny you should mention encoders. Now that I have the i/o working I checked to see if the encoders were working. Y is working perfectly. X and Z show some movement (thous or tenths) when I manually turn the screws. I've checked that the encoders have +5VDC where they should.

For debugging encoders, first thing to look at is the rawcounts pin (with halmeter)
if it only toggles back and forth one count, this indicates that one of the A/B signals
is not getting to the counter.

If rawcount counts up and down, but the DRO is wrong, then you likely have a scaling problem

x and z rawcounts only toggle back and forth one count as you describe. bad encoders or wiring issue? anyway i can check at the encoder? i dont have a scope.

Are the encoders single ended or differential?
that is, is there a single A,B and perhaps Z wire or are there a Pair for each? (A,/A B, /B and Z, /Z)

The encoder signals can be checked with a voltmeter or perhaps more easlily with a LED and a resistor

For single ended signals the LED anode should connect to 5V through a say 300 Ohm resistor and the cathode to the encoder signal

For differential encoders the LED+resistor should be connected between the A and /A or B and /B signals

Both the A and B signals should toggle when the shaft is turned slowly

I measured voltage from A+ to A- and B+ to B- at the encoder connector on the X and Z encoders. Unfortunately the Y encoder does not have a connector near the encoder. On both encoders the A readings were between 0V and .5V. The B readings on both encoders were between 3.2V and 3.8V. As I turned the screws the readings move around in those ranges. I tried the LED as well (before trying the multimeter). As expected A wouldnt light the LED and B lit it dimly.

The A pair and the B pair should behave identically , that is
all pins should have roughly TTL level swings
(with a 0-.4V low and a 2.4 to 5V high)
depending on shaft position
if the A and B pairs behave differently I would check your wiring