Hi GuitardedGeezer,

You won't hurt your 'ear' by practicing without an amp. I think it's better than playing with too many effects, you're actually hearing the tone of the guitar but many things will sound richer when you're plugged in.
With the amp, try putting the pre and post gain at about 5 and see how that effects the sustain, both of these gains will increase it.
The uneven magnets, I believe, are the way the old Stratocasters used to come and when they make newer guitars with this style, they're emulating the original single coil design. The string height should be about the same from the nut to the bridge, you may need to get your guitar tuned up by a pro, this will make it easier to play and it will stay in tune better. A guitar 'set up' usually runs $50-$100.

Neal