I would choose Japan. I've been to Japan twice and been to Kumoricon twice, the former is a much better experience for a person interested in Japanese culture.
Now, I have some advice as to were you might be able to have your cake and eat it too.
If I understood your post right, you said that you'd be going with a friend to visit his family. Chances are you would be staying with said family then? That will cost you $0 (however, buy them gifts, which you could easily keep under $30) and you might even get a meal or two out of it.
Plane tickets, if you buy them in advance enough, look to be under $1400 (now, this was for July 1st 2008 to July 31st 2008, Expedia can't go out as far as necessary). That is a fairly decent price if you aren't paying room and board.
If you plan on traveling around Japan once you are there, buy a JR Rail Pass (about $100+ a week). I payed about $400 for my last JR Pass, and got about 300% of the value back from it (that was only when I calculated the 6 Shinkansen rides I took, and not for standard trains).
Food costs can be relatively inexpensive if you stay away from tourist traps and high-end places (don't worry, the best Japanese food is in small Mom & Pop places).
Where you are going to suffer is gifts for yourself and others. However, if you have self-disipline, keeping these costs low is easy. Just buy any presents not for yourself at the 100 Yen Store.
I would say you can comfortably travel in Japan on a budget of $2000 to $2500. This is a lot, but it is definitely cheaper than most do travel there with.
Here is another tip: Pre-reg for Kumoricon before December 31! 25 bucks usually. For hotel, get some friends together and split the cost. It is doable.