CD shops are an endangered species even in Tokyo, but Disk Union is still around. Their JazzTOKYO store in Ochanomizu specializes in jazz, but other stores also have secondhand jazz CDs in stock. If you register on their website, you can search for all of their stock online, but it may be difficult if you can't read Japanese. Do you have anything in particular that you're looking for?
https://diskunion-jazztokyo.blog.jp/
If your companion isn't really into jazz, it's probably best to avoid hardcore live music venues, but places like Blue Note Place in Ebisu and Brooklyn Parlor in Shinjuku have a variety of food & drink options, and they're also run by the same company as Blue Note Tokyo, so they sometimes have live music too.
https://www.bluenoteplace.jp/
https://www.brooklynparlor.co.jp/
Even at Jazz Kissa (cafes), where talking is prohibited during the day, you can talk at night. I sometimes go to Eagle in Yotsuya, which has recently seen an increase in overseas customers. They have nice cheesecakes and strong coffee, and good huge JBL audio system.
http://www.jazz-eagle.com/index.html
If there is a particular artist you want to see and you want to go to a small live house, you should search for this site.
https://www.tokyogigguide.com/en/
Tokyo is a huge city with a huge number of live music venues scattered all over the place, so it's difficult to go from venue to venue (I miss NYC). It's better to plan in advance.
I can't drink alcohol, so I don't really know about whiskey. I heard that Tokyo Whiskey LIbrary in Minami-Aoyama has over 1300 types of whisky.
https://tokyo-whisky-library.com/
Transportation -- public transportation such as train/subway or buses(maybe a bit tricky for foreigners) are good, and these days sometimes you can use Uber, and there is an app called Go.
https://go.goinc.jp/lp/inbound
Enjoy your stay!