I've personally never been to Japan, so can't give personal recommendations.
Maybe look in the Directory on the top of this website and go to" Whisky Bars of the World". I would assume this is similar to the booklet that comes out every year with the July WM subscription, but seeing as there are no whisky bars up here, I don't really peruse it to hard.
There may be information there on Kyoto bars to frequent, but I'm not sure how the contenders are selected by WM. It may just be a list of advertisers.
Here's a link for you to peruse that may, or may not, be of some use:http://eatsdrinksandsleeps.com/2014/03/ ... oto-japan/