NT: glad you didn't take lasting offense! Re: letting chicks mingle with the flock: I think a lot depends on your flock dynamics, amount of space available, and if you have plenty of places for the chicks to get away from the older ones. I integrated chicks last year at 9 weeks without incident. Started by letting them all out to free range together. Initially, the chicks were moved from brooder/tractor in the garage to same tractor outside in the yard. They were then let out to free range. Then moved into lower level of 8 x 12 coop where they had 4 x 8 partitioned off under the hen's loft. Then, I removed the divider. This year, I've found the integration to be more difficult between chicks with 3.5 week age difference (6 older, 22 younger) I had them in the above mentioned loft with a divider, then let the littles mingle with the bigs during the day when I was around to supervise. Started that about 3 weeks ago. Then, I gave them a very small run that is inside the big flock's run, and cut some doors so the chicks could come and go at will (Thanks Azygous for the idea) They've been doing great. Jack the roo loves his babies, and will tid-bit them. The hens give a bit of chase, and an occasional peck. One of the hens got into a serious altercation with a cockrel yesterday. I doubt that he'll go near her again! So, the littles are integrated (during the day) with the big flock at 6 weeks old. It would be a bit different if they were expected to roost together. Also, key is to be sure there are plenty of feeding stations. I also use lots of scratch during integration to give them something productive to do.
Regarding your difficult hatches: I have to wonder if there is some infectious process going on. You're buying a Brinsea? Hope that solves the issue.
You should take note of infertile eggs, b/c that indicates your roo is not getting the job done for what ever reason. But, the infertiles should not count in your hatch rate IMO. This would be one time (among many) when it would be good reason to do an eggtopsy at end of hatch. No blood in an egg = no embryo development.
Could be that your Stooges were late absorbing their yolks, and therefore not hungry until just recently. Amy and I have had recent discussion regarding the yolk absorption in relation to chicks starting to eat. I'd like to suggest a new experiment: When removing chicks to the brooder, take note of the fullness of their bellies, and their overall muscle tone. Are the bellies full, and the chicks have a "plump" "heavy" feel to them? Or do they have bellies that are not as full, and they feel a bit leaner, and lighter? I've done some reading in the past regarding how those leaner chicks don't fare so well in hatchery shipping, b/c they've already used their yolk reserves. So... I'm throwing out a suggestion that we do an informal study. It would be most easily done with smaller hatches, unless you had the resources for a divided brooder. Note how soon chicks from each group start feeding. See if there's any correlation between skinny/plump chicks and the time they start actively feeding.