First, are you using the expansion boards or a stand-alone KL25Z?
It would help if you could post a screen shot of the full configuration settings window, showing all option settings, and a photo or diagram of your physical KL25Z and expansion board wiring. That would help make sure we're all talking about the same thing.
For the plunger, did you ever run the Windows "set up USB game controller" control panel and use the "Calibrate..." button? You shouldn't ever do that - it might be the reason you're seeing weird behavior in VP. If you did, you should go back to that control panel and click "Reset to default" on the "Settings" tab. If that's not it, I'll have to look at your config settings and wiring when you have a chance to post that.
You can connect LED strips to any power board output, if you're using the expansion boards. If you're using the standalone KL25Z, external circuitry is required. This is described in the v1 build guide - search for "Build the LedWiz output drivers". Once you build those circuits, you can connect LED strips or just about anything else to the MOSFET outputs.