2) Click to run is slowing down things, so yes it must be disabled and no it will not prevent applications from running.
4) It depends where you put them and what settings there are in CleanUp
5) There will be a little performance, but the question is always if you notice it or not.
e.g. 100km/h is slower than 100,05km/h, but you likely will not notice the difference although there sure is.
But as I've said many times, there is no "cleanup" tool that does anything you can't do already yourself.
I.m.o. they are all a waste of money (if you have to pay for them)