Encoder

I would first go through the INI file and change the machine
parameters (in the TRAJ, AXIS, and JOINT sections) to match your
actual machine hardware, looking at the LinuxCNC INI file
manual as you change things:

linuxcnc.org/docs/html/config/ini-config.html

If this appears too daunting, you can use pncconf to setup a sample
ini file and you can copy paste sections from that created ini file over
the basic7i97 ini file.

Ok, I have set those up to the best of my abilities. What do you suggest my next few steps be, please?

First I would de-power the drives run LinuxCNC and verify Encoder
scaling and direction in LinuxCNC DRO.

Next I would verify that you can enable/disable the drives from LinuxCNC.
That is, when you start LinuxCNC (before you go into the "machine-on" state)
The motor drives must be disabled. and only enabled when LinuxCNC enters the
"Machine-on" state.  This is a safety issue

Then I would look a a tuning tutorial  like:

gnipsel.com/linuxcnc/tuning/servo.html

Note There is a bug in the basic7i97.hal file I provided,
it is missing PWM enables for joint 1 and 2, These need
to be added:

net y-enable   => [HMOT](CARD0).pwmgen.01.enable
(in the joint 1 section)

net z-enable   => [HMOT](CARD0).pwmgen.02.enable
(in the joint 2 section)
 

awesome saying it how you just did helps me out a lot. One step at a time