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Heres where im at with the project, I got the most of the machine wired up, and had it "functioning" the hydraulic that actuates the back and forth of the shuttle is leaking threw and slowly pushes forward when idle aswell as makes a big mess of my floor. When the machine trys to shuttle forward it like jumps back and forth intill it hits the spot it needs to be on the linear encoder then slowly seeps forward. I had a feeling this would be a problem. Am I crazy to try to pair a encoder to a hydraulic and expect it to acurately position? Or would this problem be solved by fixing the leaking hydraulic and maybe a new solenoid valve. Is there any examples of somebody doing similar, controling a hydraulic accurately with a linear encoder. or do i scrap the hydraulic system, only keep it for clamping and to push the blade forward. Replacing the hydraulic with a heavy duty servo motor and ball screw. 

My PC uses a Realtek RTL8111/8168/8411 network card, integrated into the Gigabyte motherboard.

Does this network card model cause problems with Mesa?

To add to what Tommy said ...

From: linuxcnc.org/docs/devel/html/plasma/qtpl...ml#plasma:z-settings

[AXIS_Z] MIN_LIMIT should be just below top of the slats with allowances for float_switch_travel and over travel tolerance. For example, if the user’s float switch takes 4 mm (0.157") to activate then set the Z minimum to 5 mm (0.2") plus an allowance for overrun (either calculated using the equation below or allow 5 mm (0.2") below the lowest slat).

[AXIS_Z] MAX_LIMIT should be the highest the user wants the Z axis to travel (it must not be lower than Z HOME_OFFSET).

[AXIS_Z] HOME should be set to be approximately 5 mm-10 mm (0.2"-0.4") below the maximum limit.

There's a nice diagram there too.