Turn trails off and when you do have them on, leave it on 10 or 50. Also, before you save, delete trails, this is probably what you ran into since the sim will want to show the trails on load.
I agree on the delete objects a certain distance away from the main body, especially with exploding objects. At the moment, I just delete objects that are moving too fast to stay in system ASAP or after some have gone through the accretion disk.
I've set up a general rule for the accretion in that if an object is 5 AU (scaled up thats 50, further out than Plutos furthest point) out and it's clear that the object isn't in orbit or has a very long (centuries+) orbit, I delete it.