Thank you Filastruder for the quick turn around. I received my screen yesterday and it works fine.

@fcwilt Thanks. That worked. The last time I set up a machine from scratch, it was with RRF2. Still not familiar with the new commands.

Problem has been solved. The problem was me. I did not have 3 check boxes checked in Bossa 1.8 that needed to be checked. I went back and re-read the instructions on DC42's blog and fixed my error. My PanelDue is now updated.

@fcwilt Thanks. That worked. The last time I set up a machine from scratch, it was with RRF2. Still not familiar with the new commands.

I think M574 X2 S1 P"xstop" gave the endstop at max message. The X0 gave the same message as X1.

Using RRF3 latest stable.
M574 X1 S1 P"xstop"
M574 Y1 S1 P"ystop"
This gives me a reading of x an y at min when queried with M119 on the console page. When I trigger the endstops, it says x and y not stopped.
If I change the lines to
M574 X1 S0 P"xstop"
M574 Y1 S0 P"ystop"
Then M119 reports there are no endstops.
Changing the X1 and Y1 to X0 and Y0 in those lines give the endstop at max.
What should those lines be if I want M119 to read the endstops are not stopped?

I found this on the description for the Duex 5.
The Duex 5 has the following features:

5 additional TMC2660 stepper motor drivers with stall notification.
5 additional extruder heater outputs.
5 servo outputs with 5V power and 5V signal levels, sharing control channels with the heaters. So you can use unused heater channels to drive servos.
5 additional endstop inputs with indicator LEDs and 3.3V/5V voltage selection. These are also usable as outputs.
5 additional controlled fan outputs, also usable for driving LEDs etc. The output voltage may be switched between 5V, 12V and VIN.
4 uncommitted general purpose I/O pins.
12V switching regulator, for generating a 12V supply for fans, LEDs etc. when the VIN power is higher than 12V.
5 additional thermistor inputs.
Support for 2 more thermocouple or PT100 daughter boards, supporting up to 4 more sensors.
Optional 5V external power input for powering servos, fans etc.

The Duex 2 has the same feature list, just with 2 channels of everything, rather than 5. Both are supplied with the 50 way connector cable between the Duet 2 Wifi and the Duex.

So I would just use a heater and thermistor input for each tool.

Most tool changers I've seen leave the heater and thermistor with the tool. And have the other heaters and thermistors plugged into their own ports. The expansion boards have such connections for all the tools. Don't they? I would not risk burning anything on my Duet out just to do a live plug and unplug.

Yeah. It's a bummer. I have it working now on the fan2 header. Thanks for the input.

The second fan is working. But it won't work on "fan0". I am going to plug it into "fan2" and change the config for it to work as a part cooling fan and then tell my slicer to use fan2 for part cooling. For some reason the fan0 port quit working. I bought this board back before they started calling it duet2wifi.

Here is my config.g file

; Configuration file for Duet WiFi (firmware version 1.21)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool on Tue Oct 30 2018 18:17:49 GMT-0700 (Pacific Daylight Time)

; General preferences
G90 ; Send absolute coordinates...
M83 ; ...but relative extruder moves

M667 S1 ; Select CoreXY mode

; Network
M550 PV-King ; Set machine name
M552 S1 ; Enable network
M587 S"ssid" P"password" ; Configure access point. You can delete this line once connected
M586 P0 S1 ; Enable HTTP
M586 P1 S0 ; Disable FTP
M586 P2 S0 ; Disable Telnet

; Drives
M569 P0 S0 ; Drive 0 goes forwards
M569 P1 S0 ; Drive 1 goes forwards
M569 P2 S0 ; Drive 2 goes forwards
M569 P3 S1 ; Drive 3 goes backwards
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation
M92 X80 Y80 Z3200 E410 ; Set steps per mm
M566 X600 Y600 Z24 E300 ; Set maximum instantaneous speed changes (mm/min)
M203 X18000 Y18000 Z600 E1200 ; Set maximum speeds (mm/min)
M201 X2000 Y2000 Z250 E2500 ; Set accelerations (mm/s^2)
M906 X800 Y800 Z800 E800 I30 ; Set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; Set axis minima
M208 X300 Y300 Z340 S0 ; Set axis maxima

; Endstops
M574 X1 Y1 S1 ; Set active high endstops

; Z-Probe
M574 Z1 S2 ; Set endstops controlled by probe
M307 H3 A-1 C-1 D-1 ; Disable heater on PWM channel for BLTouch
M558 P9 H5 F400 T2000 ; Set Z probe type to bltouch and the dive height + speeds
G31 P25 X25 Y0 Z0.280 ; Set Z probe trigger value, offset and trigger height
M557 X40:285 Y15:280 S60 ; Define mesh grid

; Heaters
M305 P0 T100000 B3950 C0 R4700 ; Set thermistor + ADC parameters for heater 0
M143 H0 S120 ; Set temperature limit for heater 0 to 120C
M305 P1 T100000 B4725 C7.060000e-8 R4700 ; Set thermistor + ADC parameters for heater 1
M143 H1 S280 ; Set temperature limit for heater 1 to 280C

; Fans
M106 P0 S0 I0 F500 H-1 ; Set fan 0 value, PWM signal inversion and frequency. Thermostatic control is turned off
M106 P1 S1 I0 F500 H1 T45 ; Set fan 1 value, PWM signal inversion and frequency. Thermostatic control is turned on
M106 P2 S1 I0 F500 H1 T45 ; Set fan 2 value, PWM signal inversion and frequency. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 ; Define tool 0
G10 P0 X0 Y0 Z0 ; Set tool 0 axis offsets
G10 P0 R0 S0 ; Set initial tool 0 active and standby temperatures to 0C
M501

; Automatic saving after power loss is not enabled

; Custom settings are not configured

I don't have a fan plugged into the 3rd pwm controlled spot.

I switched to 24v power supply from a 12v power supply. I got a 24v heater for the hotend and 24v fans all around. Everything was working before the change. Changed everything out and power up and everything except the part cooling fan works. I checked continuity of the wire and it is good. I changed out the connectors on both ends and still the fan will not work. I tried a second 24v fan and it won't work. I plugged the part cooling fan into the port for the hot end fan and set the hot end for 50c and when the hot end gets to 45c, the part cooling fan came on. So anything else I can check?

Thanks guys. That was what I was thinking. Was planning on doing the pid tune again. Just wanted to make sure.