You don't have to clear customs but you do have to go through another security check. It isn't like transfering at Pearson where once you have gone through security to board a plane you are good. I almost missed my connection to Manila on that same flight from Toronto because I only had an hour and 45 mins. I had to run through the terminal and I was last to board. The Japanese don't seem very interested in offering any assistance even if you tell them you have a connection to make.

I was standing in a line with about 200 people waiting for the security check while watching my time to take-off drop to under 25 minutes.

I was not happy to say the least.

Make sure you know the gate by the time you get to the security line and also the layout of the terminal.

Good luck overnighting in Tokyo. Narita is a good 1.5 hours from Tokyo each way and they will likely put you up at one of the hotels near Narita. They did that to me when our flight home was cancelled and it is not worth it to try and go to Tokyo if you're only there overnight. Narita might be the main airport for Tokyo but it is a long way from the city.