I spent four years in Japan, as a high school english teacher outside Osaka. So the glasses I wear when reading your initial post frame my viewpoint through that (somewhat distant) experience.
The change has been a lot more difficult than I would have ever imagined.
Living in japan will test your maturity level, and it won't be easy. You probably won't stay there the rest of your life. So you need to formulate some goals, some achievable outcomes that you'd like to take with you when you leave. Then, while you are there, you can focus on those. It'll help to have a focus. Any focus is a good focus, but one that adds to your life later on will be more valuable. Japan is an incredibly deep, rich culture - to be jumped into and enjoyed during your time there. Jump in, both feet first. Just, know when why and how to pull the rip cord! actually, as good sky divers will tell you, they'll have a plan about when to pull the rip cord - before they even dive. That should go for all culture sky divers too. Talk to your wife about expectations as to how long you'll both stay in Japan (on this first trip), and establish a goal that'll take you a while to complete, and then evaluate when you want to leave after achieving that goal.
Her family and friends treat me very well, but I miss Canada, my mom, my friends, and all the familiarity of home.
You are lucky to have your social life figured out, and be surrounded by new family. That's a huge opportunity for delving into the culture, and doing some high quality drinking!
My Japanese is at a beginner level and I'm learning through using Rosetta Stone and just trying to talk to people randomly at stores or at restaurants.
Drop the Rosetta stone. do yourself a favor and enroll in an intensive 3 month Japanese language school. Study at least 20 hours a week in class for 3 months, followed by at least the same if not more time studying what they are teaching you as well as your own study of Kanji and grammar on your own. Take it seriously, or just leave now. Take pride in your ability to learn, and your new family will take pride in teaching you and hanging out with you. They are nervous with the english thing. Move towards their comfort zone, and out of yours.
I thought I would be able to survive socially by just having my girlfriend and her family but I feel lonely not having my friends around to talk to. I crave human contact with others who are going through the same feelings and need to have friends who I can speak to. I live in a more remote part of Japan and there are very few english speakers here.
You really have tackled a tough assignment. Look around, they'll be some foriegners somewhere! Maybe a short train ride away, but they'll be someone somewhere that'll crack a few beers and allow you to 'blow off some steam' and laugh at you confusion and hangups. It's important to get it out. Then forget about it. And, if you don't believe me, just find someone to have a couple drinks with, and they'll be 'letting it out' themselves, and you'll enjoy laughing at their hangups. Usually when one person is enraged about the Japanese system or some such thing, the other person will focus on the positives, and then next week or next month, they'll reverse roles. Its fun. Its a necessary coping mechanism, and can bring life long friendships to boot. So, look around and be willing to travel - it'll keep you healthy.