i'm not sure if this will actually help, but sometimes i just tell my kids i won't be their referee. they are only 4 and 3, but come whining and complaining about each other all the time. unless someone has broken a big rule, like hitting, i tell them they have to figure it out together. (4 yo is a girl and i've had to tell her if she really wants to keep something she has to hold on tight!)
they also know that if they can't figure out how to play with something (sharing, taking turns, one just surrendering) then i will step in and just take the toy. i'm not yelling at them and they're not in trouble, they're just not ready to play with that toy unless they can find out a system that works (i also don't usually offer suggestions, their sense of "fair" may not be accurate, but if they agree on it then it doesn't matter what i think. so far i've never had one of them bully the other into an agreement that wasn't at least mostly fair, since they both have to agree!)
my kids are also under the impression sometimes that if one is being mean i will still make them play together. i tell J (3 yo b) all the time that if he's not nice to C (4 yo g) i won't make her play with him, she can go do something else. that's usually enough to get him to be nice since he'd rather play with her than without. (i also have time set aside every day where i MAKE them play alone and just tell them they in that time they get to have their stuff all to themselves for a while. this helps them to come back and play like they haven't seen each other for a while and be nice)
sometimes i just hear them fighting and i'll go in and say "are you guys having fun?" they'll say no and i'll just tell them that they should try to do something different so they can have fun instead. usually they'll get over their fight, or i'll mention they need to work it out.
i don't know what to tell you about bed time, unless one has forgotten to brush their teeth, needs to go potty or is having pain, ours don't get back up. but they know if they do (for reasons other than those i just mentioned) they'll have time out. this happens so rarely i guess i'd just say be consistent, don't let it ever be ok to get back up and they'll figure it out.
this may not help you since you're boys are so far apart and a 9 year old can really do some damage to a 3 year old (my kids are only 11 1/2 months apart and pretty the same size, only a pound apart). But i watch when i see them playing rough and wrestling or playing rough tag and i just nicely say "wow, you guys look like you're having a lot of fun! remember that sometimes you get hurt playing like that, it's ok, but if it happens this time you can't get mad at each other and try to get each other in trouble since you are CHOOSING to play that way. Have fun!" inevitably one or the other will get hurt, and they come crying "j stepped on my finger!" and i just say, "oh that's too bad! but remember, you chose to play that way and sometimes that happens." i'll let him kiss it if he wants, but i don't really want to make them feel too bad for those kinds of little accidents. (sometimes just mentioning they're playing rough is enough to get them to remember to be a little more careful)
wow that's long. i hope it's helpful!
A.