Hi,
1. Actually we have a laptop to calculate the performance for take-off. The computer gives us flex, flap setting and speeds. You may select optimum flap and the computer will tell you which flap setting is best, or you may(for operational reasons) tell the computer which flap setting you would like to use. The important thing is that the speeds and flex corresponds to the chosen flap setting.
2. The running short of fuel happens incredibly easily. Airlines push us to carry mimimum fuel. The nav log typically allows less than 5 min contingency fuel. I have seen half this fuel used by excessive delay for take off after start. Then given that in busy airspace you probably won't get your flight level, you can very easily run into problems. The airline I fly for has had this happen a few times, especially routing through China(before they introduced more flight levels).