I keep stats for the Canadian Football League. This is how we do things up here.
1. A rush for a loss gets charged to the rusher, same as fbref2 said.
2. The lost yardage in a quarterback sack is charged to Team Losses, not the quarterback. The yards will also be credited to the defensive player responsible for the sack.
3. Penalties are recorded separately. It would only result in a 5 yard run, and 5 yards by penalty. If a first down was gained by the runner, it would count as a first down by rushing. If the penalty caused a first down, it would result in a first down by penalty.
4.
http://www.cfl.ca/CFLRulebook/scoringrules.html