David
I'm back after the show and would like to get this up and running. I have a complete installation on the big Scara now.

All of the extruder speeds have been corrected but it essentially does the same thing. It homes perfectly at relatively high speeds without a problem. Then it starts to print and everything slows down, the distal arm just slowly comes in and crashes.
  links included the G-Code and a photo of the board installation.

The prox switch is worked exceptionally well so if anyone else needs a 5 volt switch I would recommend these. We need the prox switch on the proximal base in order to do continuous rotation.
[[url]https://www.dropbox.com/s/lp2tysdk2q5g7ff/20180326_170037.jpg?dl=0]

[[url]https://www.dropbox.com/s/3sir48tk8nz2xfn/20180326_170049.jpg?dl=0]

[[url]https://www.dropbox.com/s/35qs8g7ggpwc7dt/56 TEST.gcode?dl=0]

David I'm using hybrid steppers so the voltage is not a problem because it has external power supply to the steppers. My minimum counts per Revolution is 800 selected on the hybrid steppers, I can't go any lower. So I don't use microstepping

The extruder High count might be misrepresented, I generated this file and that was left over from a print that I did on another platform. But I'll definitely check and make sure before the next test. Unfortunately I had to break it down because we have to go to a large show coming up in Pittsburgh. So I had to go back to my old platform.

link to g-code

https://www.dropbox.com/s/vsrvgqxz7i9x0yo/cyln1%282%29.gcode?dl=0

I'm able to achieve relatively high speeds, so it's completely different when it starts to run the program , it as if the processor can handle it.
Like when I'm homing or moving into position to start the print

Did you get a chance to look at my settings, it's been awhile

; SCARA #2SHOP
M111 S0 ; Debug off
M550 SCARA ; Machine name and Netbios name (can be anything you like)
M551 Preprap ; Machine password (used for FTP)
;*** If you have more than one Duet on your network, they must all have different MAC addresses, so change the last digits
M540 P0xBE:0xEF:0xDE:0xAD:0xFE:0xED ; MAC Address

;*** Networking
M552 S1 ; Turn network on

;*** Ethernet networking: Adjust the IP address and gateway in the following 2 lines to suit your network
M552 P192.168.1.14 ; (0 = DHCP)
M554 P192.168.1.255 ; Gateway
M553 P255.255.255.0 ; Netmask

M555 P2 ; Set output to look like Marlin
G21 ; Work in mm
G90 ; Send absolute coordinates…
M83 ; ...but relative extruder moves

; Disable Fan 1 thermostatic mode

M584 X5 Y6 Z7 E3 ;Set drive mapping
; Axis and motor configuration
M569 P5 S0 R0 T4 ; Drive 0 goes forwards X
M569 P6 S0 R0 T4 ; Drive 1 goes forwards Y
M569 P7 S0 R0 T4 ; Drive 2 goes forwards Z
;M569 P8 S0 R0 T4 ; Drive 3 goes forwards E
M569 P3 S0 ; Drive 3 goes backwards E
M669 K4 P453.75 D458.75 A-90:90 B-156:156 C0:0:0 T1 ; set SCARA mode and parameters
;M669 K0;

;Endstop configuration
M574 X1 Y2 Z2 S0 ; M574 X2 Y2 Z2 S1set endstop configuration (all endstops at high end, active high)
;*** The homed height is deliberately set too high in the following - you will adjust it during calibration

M666 X0 Y0 Z0
M208 S1 X-90 Y-126 Z-1 ; Axis minima
M208 X90 Y1156 Z150 ; Axis maxima Z WAS 100 ; put your endstop adjustments here, or let auto calibration find them
M350 X1 Y1 Z1 E16 E2 I1 ; Set 1x microstepping with interpolation
M92 X736.36 Y736.36 ; Steps/degree for proximal and distal joints M92 X415.726492 Y273.504273
M92 Z6600 E350 ; Steps/mm for Z and E
M906 X0 Y0 Z0 E1500 I60 ; Set motor currents (mA) and increase idle current to 60%
M201 X100 Y100Z1000 E1000 ; Accelerations (mm/s^2)
M203 X1000Y1000Z5000 E1000 ; Maximum speeds (mm/min) 1000
M566 X10 Y10 Z500 E1200 ; Maximum instant speed changes mm/minute

M581 Z1 S1 C1 ;Configure external trigger

; Thermistors
;M305 P0 T100000 B3950 R4700 H30 L0 ; Put your own H and/or L values here to set the bed thermistor ADC correction
;M305 P1 T100000 B3974 R4700 H30 L0 ; Put your own H and/or L values here to set first nozzle thermistor ADC correction
;M305 P2 T100000 B3974 R4700 H30 L0 ; Put your own H and/or L values here to set 2nd nozzle thermistor ADC correction

; Tool definitions
M563 P0 D0 H1
G10 P0 X0 Y0 Z0 ; Set tool 0 axis offsets
G10 P0 R00 S00 ; Set initial tool 0 active and standby temperatures to 0C

M92 E663:663 ; Set extruder steps per mm

;*** If you are using axis compensation, put the figures in the following command
;M556 S78 X0 Y0 Z0 ; Axis compensation here

M208 S1 Z200 ;M208 S1 Z-0.2 ; set minimum Z

;T0 ; select first hot end

; Pressure advance
;M572 D0 S0.5

; Misc
M83
M117 Use https://configurator.reprapfirmware.org/ to set up your printer config
M302 P1
M563 P0 D0 T1 ;enable cold extrusion.

; Heaters
;M143 H1 S260 ; Maximum heater temperature
M140 H-1 ; No bed heater
;M305 P1 T100000 B4138 C0 R4700 ; Thermistor parameters for heater 1
;M307 H1 A577.0 C199.0 D9.8 S1.00 B0
M665 H100
TO

David I was able to reduce the steps per/ degree down to 736. You were correct because after adjusting some parameters I was able to hold connection over WiFi and complete the Homing sequence. The scara moves at a good fast rate during the Homing sequence, but now the problem is as soon as the print starts it slows down to less than a snail's pace. No matter what speed I set in the g code it just barely moves , it's as if the processor is choking. What do you think

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M122 link
https://www.dropbox.com/s/k0xfx3e99gpzeey/M122.txt?dl=0

MaxReps: 0, StepErrors: 0, FreeDm: 240, MinFreeDm 240, MaxWait: 0ms, Underruns: 0, 0

Micro stepping is set at 1 and the Homing speed is relatively slow.
M92 is 23563.7373. Steps / degree