Since I cut guitars I use the Y axis as my 39" and the X 25".
The pin out on my control box is a little bit diffrent than the new KG but you should only have to change the "motor outputs" "Dir LowActive" and "Step LowActive" to change there directions.
Once in awhile I'll wonder why my machine isn't running smooth and come to find I forgot to have it in "Constant Velocity" mode.
If your Limit switch's go off for no reason change your "Deboucne Interval" to around 800+, or turn off "Watch Dog"
One thing that took me awhile to get the hang of was the "Softlimits" let me know if you have any trouble and I can post some advice about them.
The "Click" sound your getting is the encoder continually checking it's position, this is okay. I hadn't thought of it till it was completely quiet in my shop and there I heard it. You can fine tune your Gecko's but I don't believe it effects anything.
There is nothing better than Mach. Benny and others are designing some amazing screens and Art and Brain are continually adding more abilities and componets to Mach. It is the best program and is not just limited to controlling CNC machines.
I didn't like K2's vacuum system so I bought some plexy glass, screws(much simpler just to use aquarium glue) and a dryer vent.
Used my K2 to cut out a hole and $10 later I had a great vacuum system. It's not pretty but works great, I need to see the bit and easly change it.