Vickewhite:
I don't press and hold the on/off button at all. I was only refering to the time it takes to shutdown after using the shutdown menu item. Keeping the power button pressed for a long period is usually a technique for forcing a complete power down and restart. I only use the power button to turn it on, holding it for a couple of seconds until the power light shows (if I'm on battery). Using the option to shutdown from the Start Menu is the best way to shut down.
Imaging the system - I'd only do that when you've got a system that's working well. For example before the bi-annual windows updates I would do one so I can revert easily if the update goes wrong. Once I know the update is OK, I'll do another so that if I do something stupid or things go wrong then I know I can at least get back to a setup I know is OK.
I'm not clear what you mean about the pen - I would stick to the drivers from the support pages.
However, if you have installed the Wacom Feel driver from the Wacom website this could be the problem. The Yoga Book needs an old version - newer versions create havoc with the Yoga Book. It's cropped up here a number of times. Lenovo don't have it on their support pages.
I would suggest sticking to how things are working, or not, with the supplied Lenovo pen for now here. Once that is sorted out you could look at previous posts about which other pens can work well the Yoga Book if you want an alternative.
I suspect the best option might be to do a complete fresh re-install but I have always been reluctant to suggest it to anyone because of the care needed in getting the drivers installed properly afterwards. FarisJayyousi has previously posted links to advice about how to do this. I've never done it myself so wouldn't try and advise on that.