Gantry machine progress

join0 to tune0 to x one rotation of the motor axis 10mm correct(encoder scale 800)
joint1,joint2 to tune1,tune2 to y1,y2 one rotation of the motor axis 7298mm (encoder scale 800)common P>I>D>settings

For Y1 ou seem to be choosing the PID gains from the [JOINT_2] section (and I wouldn't) and the encoder scale from the [JOINT_1] section (and I wouldn't

But the main error is that you are setting the scale of encoder.01 in the joint.02 section.

#----y1---


setp pid.y1.Pgain [JOINT_1]P
setp pid.y1.Igain [JOINT_1]I
setp pid.y1.Dgain [JOINT_1]D
setp pid.y1.bias [JOINT_1]BIAS
setp pid.y1.FF0 [JOINT_1]FF0
setp pid.y1.FF1 [JOINT_1]FF1
setp pid.y1.FF2 [JOINT_1]FF2
setp pid.y1.deadband [JOINT_1]DEADBAND
setp pid.y1.maxoutput [JOINT_1]MAX_OUTPUT
setp pid.y1.error-previous-target true

net y1-index-enable <=> pid.y1.index-enable
net y1-enable => pid.y1.enable
net y1-pos-cmd => pid.y1.command
net y1-vel-cmd => pid.y1.command-deriv
net y1-pos-fb => pid.y1.feedback
net y1-output => pid.y1.output

# ---PWM Generator signals/setup---

setp hm2_5i25.0.7i77.0.1.analogout2-scalemax [JOINT_2]OUTPUT_SCALE
setp hm2_5i25.0.7i77.0.1.analogout2-minlim [JOINT_2]OUTPUT_MIN_LIMIT
setp hm2_5i25.0.7i77.0.1.analogout2-maxlim [JOINT_2]OUTPUT_MAX_LIMIT

net y1-output => hm2_5i25.0.7i77.0.1.analogout2
net y1-pos-cmd joint.2.motor-pos-cmd
net y1-enable joint.2.amp-enable-out

# ---Encoder feedback signals/setup---

setp hm2_5i25.0.encoder.01.counter-mode 0
setp hm2_5i25.0.encoder.01.filter 1
setp hm2_5i25.0.encoder.01.index-invert 0
setp hm2_5i25.0.encoder.01.index-mask 0
setp hm2_5i25.0.encoder.01.index-mask-invert 0
setp hm2_5i25.0.encoder.01.scale [JOINT_2]ENCODER_SCALE

net y1-pos-fb <= hm2_5i25.0.encoder.02.position
net y1-vel-fb <= hm2_5i25.0.encoder.02.velocity
net y1-pos-fb => joint.2.motor-pos-fb
net y1-index-enable joint.2.index-enable <=> hm2_5i25.0.encoder.02.index-enable
net y1-pos-rawcounts <= hm2_5i25.0.encoder.02.rawcounts

# ---setup home / limit switch signals---

net y1-home-sw => joint.2.home-sw-in
net y1-neg-limit => joint.2.neg-lim-sw-in
net y1-pos-limit => joint.2.pos-lim-sw-in

is this the right values?

No, you are still over-writing the values for encoder.01 in the Y1 section rather than setting the values for encoder.02

if you do thinks with out now what you are doing this is what happens
#*******************
# JOINT Y0
#*******************

setp pid.y0.Pgain [JOINT_1]P
setp pid.y0.Igain [JOINT_1]I
setp pid.y0.Dgain [JOINT_1]D
setp pid.y0.bias [JOINT_1]BIAS
setp pid.y0.FF0 [JOINT_1]FF0
setp pid.y0.FF1 [JOINT_1]FF1
setp pid.y0.FF2 [JOINT_1]FF2
setp pid.y0.deadband [JOINT_1]DEADBAND
setp pid.y0.maxoutput [JOINT_1]MAX_OUTPUT
setp pid.y0.error-previous-target true

net y0-index-enable <=> pid.y0.index-enable
net y0-enable => pid.y0.enable
net y0-pos-cmd => pid.y0.command
net y0-vel-cmd => pid.y0.command-deriv
net y0-pos-fb => pid.y0.feedback
net y0-output => pid.y0.output

# ---PWM Generator signals/setup---

setp hm2_5i25.0.7i77.0.1.analogout1-scalemax [JOINT_1]OUTPUT_SCALE
setp hm2_5i25.0.7i77.0.1.analogout1-minlim [JOINT_1]OUTPUT_MIN_LIMIT
setp hm2_5i25.0.7i77.0.1.analogout1-maxlim [JOINT_1]OUTPUT_MAX_LIMIT

net y0-output => hm2_5i25.0.7i77.0.1.analogout1
net y0-pos-cmd joint.1.motor-pos-cmd
net y0-enable joint.1.amp-enable-out

# ---Encoder feedback signals/setup---

setp hm2_5i25.0.encoder.01.counter-mode 0
setp hm2_5i25.0.encoder.01.filter 1
setp hm2_5i25.0.encoder.01.index-invert 0
setp hm2_5i25.0.encoder.01.index-mask 0
setp hm2_5i25.0.encoder.01.index-mask-invert 0
setp hm2_5i25.0.encoder.01.scale [JOINT_1]ENCODER_SCALE

net y0-pos-fb <= hm2_5i25.0.encoder.01.position
net y0-vel-fb <= hm2_5i25.0.encoder.01.velocity
net y0-pos-fb => joint.1.motor-pos-fb
net y0-index-enable joint.1.index-enable <=> hm2_5i25.0.encoder.01.index-enable
net y0-pos-rawcounts <= hm2_5i25.0.encoder.01.rawcounts

# ---setup home / limit switch signals---

net y0-home-sw => joint.1.home-sw-in
net y0-neg-limit => joint.1.neg-lim-sw-in
net y0-pos-limit => joint.1.pos-lim-sw-in


#----y1---


setp pid.y1.Pgain [JOINT_1]P
setp pid.y1.Igain [JOINT_1]I
setp pid.y1.Dgain [JOINT_1]D
setp pid.y1.bias [JOINT_1]BIAS
setp pid.y1.FF0 [JOINT_1]FF0
setp pid.y1.FF1 [JOINT_1]FF1
setp pid.y1.FF2 [JOINT_1]FF2
setp pid.y1.deadband [JOINT_1]DEADBAND
setp pid.y1.maxoutput [JOINT_1]MAX_OUTPUT
setp pid.y1.error-previous-target true

net y1-index-enable <=> pid.y1.index-enable
net y1-enable => pid.y1.enable
net y1-pos-cmd => pid.y1.command
net y1-vel-cmd => pid.y1.command-deriv
net y1-pos-fb => pid.y1.feedback
net y1-output => pid.y1.output

# ---PWM Generator signals/setup---

setp hm2_5i25.0.7i77.0.1.analogout1-scalemax [JOINT_1]OUTPUT_SCALE
setp hm2_5i25.0.7i77.0.1.analogout2-minlim [JOINT_2]OUTPUT_MIN_LIMIT
setp hm2_5i25.0.7i77.0.1.analogout2-maxlim [JOINT_2]OUTPUT_MAX_LIMIT

net y1-output => hm2_5i25.0.7i77.0.1.analogout2
net y1-pos-cmd joint.2.motor-pos-cmd
net y1-enable joint.2.amp-enable-out

# ---Encoder feedback signals/setup---

setp hm2_5i25.0.encoder.02.counter-mode 0
setp hm2_5i25.0.encoder.02.filter 1
setp hm2_5i25.0.encoder.02.index-invert 0
setp hm2_5i25.0.encoder.02.index-mask 0
setp hm2_5i25.0.encoder.02.index-mask-invert 0
setp hm2_5i25.0.encoder.02.scale [JOINT_2]ENCODER_SCALE

net y1-pos-fb <= hm2_5i25.0.encoder.02.position
net y1-vel-fb <= hm2_5i25.0.encoder.02.velocity
net y1-pos-fb => joint.2.motor-pos-fb
net y1-index-enable joint.2.index-enable <=> hm2_5i25.0.encoder.02.index-enable
net y1-pos-rawcounts <= hm2_5i25.0.encoder.02.rawcounts

# ---setup home / limit switch signals---

net y1-home-sw => joint.2.home-sw-in
net y1-neg-limit => joint.2.neg-lim-sw-in
net y1-pos-limit => joint.2.pos-lim-sw-in
is this near to what i try to fix?

This looks wrong too:

setp hm2_5i25.0.7i77.0.1.analogout1-scalemax [JOINT_1]OUTPUT_SCALE
setp hm2_5i25.0.7i77.0.1.analogout2-minlim [JOINT_2]OUTPUT_MIN_LIMIT
setp hm2_5i25.0.7i77.0.1.analogout2-maxlim [JOINT_2]OUTPUT_MAX_LIMIT