I'm with abmj-jr; for $84, the Toronto transfer on Canadian beats the heck out of flying all the way to Beijing (which is a HUGE airport and can be hard to get around) to get to Japan. Last time I transited a China airport (in my case Shanghai) they did make me clear immigration and customs both inbound and outbound. Lines were huge. I had to assert myself to make it in 2+ hours and that was only with carry-on.

I still would take the two one ways for $1,000 over both of those options. By flying into Osaka, you only need to go one way (to Tokyo) via train which will will save you enough to make getting the JR pass unnecessary. You're only there 7 days. Between Tokyo, Osaka, Kyoto, and a possible side trip to Nara, you can easily fill a week. The savings by taking the direct flights instead of buying a JR pass is easily over $100 even counting paying for transit to/from airports, so that covers a goodly chunk of the fare difference.

Incidentally, the non-stop bus between Haneda airport and the nearest bullet train stop (shin-Yokohama) takes in total more like 50-60 minutes considering the wait for the bus and actual transit time. I know because I just did this two weeks ago at a low traffic time. It can take a lot longer if you have to wait in line to buy the bus ticket instead of realizing you can go straight to the platform and buy it there from a machine if you have Yen.