Good extracting temperature - The warmer the better, 80-90 is good. It flows faster. Faster flow leads to your next question.
As far as speed, you don't want to go too fast, you could blow out the foundation. Just go for a comfortable speed, heat is your friend, if it's warm, the honey comes out faster and less damage to the combs.
Empty hive body is great, I'm not sure I understand what shed space has to do with lids. Put them on top of newspaper and put a lid on the top.
I don't have a hot knife either, you can use a bread knife something serrated is best. Just keep a pan of hot water, Put the knife in it between uncapping.
When you say some of the cells didn't get emptied, do you mean they didn't get uncapped? Use an uncapping fork to scrape open the capped cells.
the bees will fix it all in the spring.