Steppers Not Moving / Mapped Wrong

Hi Friends, 

Just getting my machine powered up for the first time and i have a list of things that aren't working and im trying slowing to knock each one of them out. I have a Queenbee pro that i converted to a XYZC machine powered with a 7i96s. I carefully labeled all the signal wires as i wired everything up and now once i get LinuxCNC up and running and try to jog to test each axis most don't work or are mapped wrong. The only one that acts somewhat as expected is X and its loud and makes a grinding noise and moves very slow. 

Regarding their mapping, when I go to jog Z i get movement from the second y motor. It makes the same awful noise and moves slow, which i'd expect because its the same motor with the same settings as the X motor. I also have a C servo that i haven't gotten anything from so far. 

Any suggestions as where to start here? can i leverage HalShow? should I just switch the motors in the electrical cabinet until the Y button moves the Y axis? I feel like i would prefer to understand whats happening and i dont feel like i do yet. Is there a way to easily reconfigure the motors without running pncconf again? 

Posting your hal and ini files would make this easier to diagnose

How are the drives wired to the 7I96S?

(TB2 pin numbers to drive signal names)

Both files attached. 

I thought i had mapped the
board step/dir 0 -> X
step/dir 1 -> y1
2->z
3->c
4 ->y2
(i hope this is what you mean by how is it wired).

The encoder i am not even worried about yet i just want the machine to move and everything to register right now.

The hal file shows mapping:

JOINT STEPGEN  AXIS

0         0           X
1         2           Y
2         4           Z
3         3           A

Thanks for your quick reply.

can you enlighten me as to how you found that out? what lines in the hal can i modify to get them correct? Also can you tell me the difference in LinuxCNC between joint and stepgen?

Also, i am fairly certain i added the second Y motor in the configurator, does it not like repeat setups?

It does not look like you setup a tandem axis in pncconf:

[KINS]
JOINTS = 4
KINEMATICS = trivkins coordinates=XYZA

[TRAJ]
COORDINATES = XYZA
MAX_ANGULAR_VELOCITY = 0.50
DEFAULT_ANGULAR_VELOCITY = 0.05
LINEAR_UNITS = inch
ANGULAR_UNITS = degree
DEFAULT_LINEAR_VELOCITY = 0.10
MAX_LINEAR_VELOCITY = 1.00

Note that the stepgen number is completely arbitrary but joint <==> axis mapping
must be setup in the kins/trajectory sections of the ini file in addition to the
hal file.

Here is how I knew Z was mapped to joint 2 and stepgen 4
#*******************
# AXIS Z JOINT 2
#*******************

setp pid.z.Pgain [JOINT_2]P
setp pid.z.Igain [JOINT_2]I
setp pid.z.Dgain [JOINT_2]D
setp pid.z.bias [JOINT_2]BIAS
setp pid.z.FF0 [JOINT_2]FF0
setp pid.z.FF1 [JOINT_2]FF1
setp pid.z.FF2 [JOINT_2]FF2
setp pid.z.deadband [JOINT_2]DEADBAND
setp pid.z.maxoutput [JOINT_2]MAX_OUTPUT
setp pid.z.error-previous-target true
# This setting is to limit bogus stepgen
# velocity corrections caused by position
# feedback sample time jitter.
setp pid.z.maxerror 0.000500

net z-index-enable => pid.z.index-enable
net z-enable => pid.z.enable
net z-pos-cmd => pid.z.command
net z-pos-fb => pid.z.feedback
net z-output <= pid.z.output

# Step Gen signals/setup

setp hm2_7i96s.0.stepgen.04.dirsetup [JOINT_2]DIRSETUP
setp hm2_7i96s.0.stepgen.04.dirhold [JOINT_2]DIRHOLD

Note that I would not edit the hal file at this point as so much is missing.
I would make sure you select the proper kinematics and setup the tandem
axis in pncconf.

totally make sense thanks for your help.

I just went to restart the pncconf and i only have three options when it comes to kinematics: XYZ, XYZA, OR XZ lathe. I believe i am missing some options here in this drop down.

edit: im stupid, trying again now. 

okay update. 

I reran the pncconf, reassigned the second y as a tandem and also corrected what turns out was mis-assignment by me initially. Everything should be good to go now in terms of what the board thinks is assigned and what is actually. Updated hal and ini attached. 

Still no movement from any axis:
X: Does nothing physically but machine thinks its jogging (DRO updating)
Y: Throws an error: "Cannot Jog Joint 1 because home_sequence is synchronized 
Z:Does nothing physically but machine thinks its jogging (DRO updating)
A: Does nothing physically but machine thinks its jogging (DRO updating)

Y cannot jog until it is homed.