Mosquito’s in Mid to Late October

Travelling across japan for two weeks from tokyo to takayama to kyoto to osaka to koyosan to hiroshima and then home. I was unable to get japanese encephalitis jab in time.

Am i in danger? What are the mosquitos like around this time?

Depends on the rain , stagnant water situation.
After the typhoon 1-2wks ago, I felt some bites..nothing too serious.

I've never, ever paid attention to that warning about encephalitis. First, once colder weather hits, they'll practically disappear. Also, once the rice fields are harvested, their breeding grounds are much reduced. Rice harvest varies, but by mid-October everywhere should be finished. Furthermore, with the probably temperatures during that time, and the fact that you seem to be in big cities for most of your trip, I wouldn't worry about it at all. If you are worried, just get some bug spray for anytime you're outdoors.

Thats a relief, it would cost me 200 pounds to get it done this close to the date and really didnt want to have to do it

It's a risk wherever mosquitos are. Being smart and preventing them is enough, but you really wont have to worry much when you're going. Bring or buy some bug spray and you'll be set.

To be honest, I do get mosquitos bites in Greater Tokyo even in November if I stay in a forest-y area for a while, such as small bush-y parks with few people. But the thing is that we tend to start covering ourselves with long sleaves and socks by mid October, so the risk of getting bit becomes smaller. I also don't think it's that common for a mosquito bite to lead into encephalitis. So either way, don't panic if you happen to be bit. The itch will even go away by washing the bitten area with water.

My mosquito bite from the jr rail train is still red after 2 days. Really you can get bites indoor or outdoor.

I remember getting bitten once on the street outside Tokyo Governmental Building in Shinjuku. On tthe tower view top floor I had gotten a huge bite mark but no disease so far. That was in early October 2013.