1. Not positive about this but as they are such low rpm fans I would just run them at full speed. Doubt it will make any difference in actual noise tbh. It is really just trial and error, connect them up and lower the voltage then monitor how high the temp of the LT goes.
2. Yes, there is a funtion called "startboost" which you can customize to apply any % of voltage for any amount of time to start the fans up.
3. Yes you can set alarms to do pretty much anything, not positive but I think the atx standby and break adapter may be a little redundant as you can use soft commands (Keyboard Sleep and Keyboard Power) within the Alarm Actions to put the system to sleep and turn it off. I guess the only thing you would use it for it to shut the system down instantly but again most motherboards will do this anyway if the temp get too high.
I think you will love the kit but be prepared for a few hours of tinkering, there are so many functions to the software it will take some time to get to know it all.