Glass scale linear encoders and steppers

The encoders are now working pretty well, but still playing with the pid tuning a little I have a question. In my hal file i am l;oading 3 encoders ( loadrt hm2_eth board_ip="10.10.10.10" config="firmware=hm2/7i76/7i76e.BIT num_encoders=3 num_pwmgens=0 num_stepgens=3 sserial_port_0=2xxxx" ) however I am using 3 linear encoders and a MPG pendant. The pendant is loaded with a custom hal file that i have attached. Should I have the card set to 4 encoders? Is the way I have it causing a possible problem? Just trying to wrap my head around all of this.

Do you still have any problems?
You can leave the handwheel on this input. That's okay. The encoder inputs can only read higher resolutions. Not necessary with the handwheel. Save it for your 4th axis in future.
Another possibility would be to set your handwheel to pulse / mm. I've attached an example. The ilopass prevents the jerk.  I have 1mm / pulse and runs very well. But adjust the scale to your data. For safety, you can comment the net "net mpg-selected-count        <= ilowpass.0.out" line and check the ilowpass data in halshow.

It’s working pretty well, thank you. The stepper pid can be tuned better I’m sure, but it’s working well. I have done all the tuning without halscope. I am having a hard time plotting with halscope, I can’t get it to work right for me. I did a bunch of reading on halscope today and I will give it another try when I get back to the machine in a week or so.