I do see your point, and it is one that many struggle with. Why does a good God do bad things or allow bad to happen? Even many Christians struggle with that concept. Can you cite an instance where Gods punishment was not justified? And how can we say He was unjustified if us human beings cannot comprehend an eternal, all powerful, immaterial being's nature? In my faith, I trust that God is sovereign over all things, good and bad as we perceive them.
As far as the relationship, I'll say for myself that I ask sometimes daily why He wants anything to do with little old me and why he puts up with my crap...why do I deserve His grace? I've heard God speak directly to me twice, audibly and directly, and one of those times at a very low and humbling point in my life I asked Him that question...why give me your grace, and He said "it's alright son, I've got plenty". Call me crazy, it happened. So why does He want a relationship with me? I have no idea, but I'm glad He does.
I'm curious, how many Christian's have you had this exact conversation with?! I like it, you're forcing me to think about the tough stuff. We should never grow so comfortable in our beliefs that we never step back and think about why we feel the way we do :)