I'm going to need to answer these in the reverse order and I'm going to assue you're probably going to be blowing these up quite large.

• If you're going to move the camera several feet to get the shots you want, you're going to get some sort mismatch when you stitch. If you're then going to blow the pictures up large, it's very likely going to look some degree of bad along a seam. How to mitigate this is really to either just do smaller pano's or find a 360 degree spot. There's alot of things that will determine how bad or not bad this will be - largely based on the particular field of view you have, but make sure to have as much overlap there as possible.

• Choosing your focal length is probably your biggest decision as it drives a few other things. The higher you go, the more impressive its going to be. When you've got a city pano and the viewer realizes they can see the guy in the office building staring out two streets away, its a neat feeling. BUT, it comes at a cost. Its significantly harder to shoot and takes much longer - which means your light can change a lot over your total shoot.

• If time isn't a factor and you can spread it out over several days to do a high focal length shoot at sunrise or sunset - its going to be much more impressive than a few wide angle midday shots. The light at sunrise and sunset is just much better. If you can isolate the sun in a single frame, it will alleviate some of the problems, get it when its behind a building perhaps. Or you could plan several shoots to combine together at twilight, just after the sun has gone done.

You should definitely be setting manual mode, and if you don't have a good tripod/head, consider renting some decent gear, it will make your life easier.