You should definitely buy tickets to the War Rooms in advance if you want to go there. My reaction was that it's a skippable sight (and an expensive one) if it's just the bunkers you're interested in. The Churchill Museum is very good; I spent hours there. It's definitely worth the time and money if you are interested in that part of the sight. A full visit can take 4 hours or more.
I have never been inside St. Paul's or Westminster Abbey, so I have no idea how long those visits would take or what the ticket situation is.
Edited to add: Westminster Abbey and the Churchill War Rooms are very close together. St. Paul's is about 2 miles from the Abbey and 1.4 miles from the Premier Inn County Hall. So St. Paul's is the outlier. All of those places are walkable if you like to walk. Allow extra time to get to the War Rooms, which are set well off the road and not as well-signed as they could be.
There are trains to Canterbury from St Pancras, Charing Cross and Victoria Stations. Many, many trains. Travel times vary, with St. Pancras having the fastest trains, but there is variation even from that station. You can easily check schedules at nationalrail.co.uk. There are a couple of stations in Canterbury, Canterbury East and Canterbury West. You can take a look at Google Maps to see where they are vis-à-vis the historic center; there's not much difference in the walking time to the cathedral. As you can see, CW should be called "Canterbury North" and CE should be called "Canterbury South".
I day-tripped to Canterbury by train a couple of years ago. It was easy to do. The tourist office runs walking tours in the historic center; I believe they were offered at least twice a day. There may have been more than one itinerary. The center is touristy but very picturesque; I spent considerable extra time walking all the streets of that area, not all of them being tourist-clogged.
There's a stained glass museum upstairs in the cathedral (no elevator) that I found very interesting. There's a modest fee for it. It was great to be able to see the glass at eye level.