Most of what I've read says to have your incubator ready to go. Just set the eggs "fat end" up in room temperature for about 4 hours and then transfer to the incubator. I've read to set them in room temperature for up to 16 hours, but I have not done that.
The eggs I have in the incubator now I set for about 5 hours air cell up in room temperature, then put in the incubator and they are doing great - healthy embryonic development from what I can tell, so far! YAY!
The only other thing I would suggest is maybe using at least one more thermometer - different brand; maybe different type thermometer. I see you're using a digital, maybe try a mercury thermometer or another digital from a different manufacturer, just to have a second temp reading source in case your digital is a tad off. I found this out the hard way and relied on one digital probe thermometer. It is about 1.5*F off compared to the other two. So, that thermometer would read 99.5, but the temp is actually 98.0 - you can see how this might be a problem.
I got a bit off topic - to directly answer, I wouldn't shut down the incubator - keep it running as close to 99.5 as you can. Also, yes, definitely candle them before putting in. Sometimes you can identify problems this way and keep an extra close eye on the questionable ones.
