depends what you're training, or what you think is your weakness. Small rungs will get you stronger fingers. Stay on the big rungs and progress through the gaps, 1-2-3, 1-3-5, 1-4-7, 1-5-9 etc improves something else (i don't know what to call it "ability to use a campus board"). If you're just concentrating on power then I don't think the rest time is a big issue, you need to recovery between sets to an extent and 4mins ain't too long. As you improve you may recover quicker and want to pack more movement into a session, so shorter rests.
Personally I stay on the big rungs because small holds isn't my weakness but big campus moves are.