Hm, I love bidding on YAJ and I did it quite often now and never take notice of the shipping prices inside Japan, but I never get fooled so far.
I use
http://www.shoppingmalljapan.com/ and I'm satisfied with them. Their fees aren't too high, they're ok and they're fast on handling your bidding, paying and sending your package out. You also have to choose and say how and when you wanna be your items send to you, that's a good service, you truly have control over everything.