Please stick with adjusting the settings in linuxCNC at this point.
I would not recommend adjusting the west amp amplifiers. Those amplifiers are a black hole of historasis . I asked jambly if the system was smooth before he started the conversion, he said they worked fine.
I started adjusting my we stamp amplifiers in my conversion. I ended up using an old ocilloscope to rough in my settings, then I was able to get ohm settings for the six pot circuits on the amos from a retired anilam repairman. I removed each amp and bench tuned the amps with an ohm meter and beads of sweat.
Never. Again. Those are an abyss I recommend staying out of . ; )
The link PCW gave is good to start with.
Wikipedia has good resources to learn about pid tuning.
Andy paugh had a great post here about pid tuning related to a cars cruise control.