It's easy to forget that Jupiter doesn't appear as a static ball, like many rocky planets do.
I was musing about it last night, and I've decided that the safest place to build a permanent base within our solar system would be in low orbit (and low inclination of orbit) around Jupiter. The massive/strong magnetic field would protect us from particle radiation that is the byproduct of nearby supernova explosions. There's still the whole asteroid/comet collision thing (Shoemaker-Levy 9, anyone?, but now you're an orbiting colony, and you can alter your trajectory. Then you've only got several million other engineering problems to worry about! Food for thought.
That is correct, and swept under my rug of "several million other engineering problems to worry about". Everything you mentioned is thought to be solvable, as best I know.