1) [edit: FIXED] Yes, if a house is vacant it costs negative rent. Since it happens rarely I never noticed. It should be something like -1 instead I think.
2) [edit: FIXED] Yes, but then you're missing a lot of factory income and won't be making positive income most likely. The general idea is that you set the price at which those goods are sold in your city. There is demand and everything you don't produce (or don't produce enough) will be imported. But it looks like there are some issues. Looking into it. It should probably actually work like this:
There is demand. Demand is controlled by the price you set. When you don't produce some item, it will be imported but at a higher price. If you overproduce that will go to waste (finacially).
3) [edit: FIXED] Will check it out.
4) [edit: FIXED] There is an extra cost of piping (+1 cost for every 5 pieces of road). I will add short description text for each of the expense rows.
5) Interesting. Most likely the market your house considers nearest is already full by the time it gets to that house.