Well, that system is pretty much depreciated. The old JS API of Linux does not accommodate much, and certainly not force feedback. I planned to remove those files - guess I haven't gotten around to it if they are still there.
I'm not sure what you mean about a y-axis issue. OIS axes should be in the range of -32k to 32k. There may be a scaling issue within OIS for Joystick axes that don't adhere to that on Linux, it would be better if you added some logging code in the Joystick event classes and dumped out what the raw values are for your device.
As for calibration, there is no inbuilt system for OIS to calibrate devices. On Windows, it is done by control panel, and I'm not aware of a Linux method for calibrating with event structure. However, all calibration is really supposed to do is move the deadzone, not really adjust the ranges of axes. Mostly, games should account for deadzones themselves, either ignoring low values, and/or letting the user calibrate values via an in-game system.