Agreed - if this really is 2 hours as the time states this is far too risky. JAL has a 1 hour check-in cut-off, so your actual window is 1 hour. 20-30 mins for bags, 5-10 mins to get to the JAL counter and actually check-in. So with an on-time arrival and everything going to plan you've got maybe 20 minutes to spare. Even a slight delay anywhere along the way (WN arrival, getting a free gate, bags, check-in, etc) and you're going to be stuck in SF.

3 hours puts you into the realms of possible, but personally I still probably wouldn't be risking that onto an international flight, especially with bags.